11 Best Cheap Hotels in San Francisco near Pier 39

San Francisco is an iconic city, steep in deep lore. Whether you’re a history enthusiast, a movie buff, an aspiring artist, or simply someone who loves traveling, you’ll love San Francisco. Each trip reveals something new, whether it’s enjoying the city from the height of Dolores Park, or walking around Chinatown. But the real buzz is in the Bay Area. It’s where we can easily visit the Golden Gate Bridge, take a cruise to Alcatraz, and check out the Fisherman’s Wharf in one sweep. The Bay Area is also where Pier 39 is. With all of the interesting tidbits about SF, sometimes we’d just like to shop, have some seafood cuisine, and check out the sea lions at Pier 39. While San Francisco can be pricey, don’t worry—we’ve found some of the best cheap hotels in San Francisco near Pier 39 so you can enjoy the city without overspending!

The Wharf Inn

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Best location. Starting strong on our list with The Wharf Inn. It’s one of the closest hotels to Pier 39 that we could stay at without blowing our budget. From the hotel, Pier 39 is only 2 blocks away, and we could easily walk there in 5 minutes. So, location-wise, The Wharf Inn has it in the pocket. Furthermore, given the affordable price point, we were thoroughly impressed by how excellent our experience was here. For starters, the services and hospitality were simply exemplary. The hotel sports a classic cozy look. It wasn’t the most modern-looking, but it only made the hotel feel more homey to us. Most importantly, the hotel was clean and well-maintained.

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Since it’s located near the water, some rooms have a partial Bay view, which we were lucky to get. Our room had a quaint balcony, a plush bed, and space big enough for an extra sofa bed. The room amenities were also great. We got a smart TV with Netflix, a coffee machine, and a mini-fridge. The area can be quite noisy though, but the room had a Modio, a device that plays white noises to help us relax and sleep better.

Lastly, the hotel didn’t have breakfast options, but we did get complimentary hot beverages. Plus, there’s a 7-11 just across the street. Or we could get breakfast at any of the nearby restaurants. Overall, The Wharf Inn is definitely a hotel with tons of conveniences.

Cow Hollow Inn and Suites

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Cow Hollow Inn and Suites is located in Marina District, on the busy Lombard Street. While Pier 39 is a 10-minute drive away, we could walk to Marina Green and Fort Mason. Plus, catching a bus to get around was pretty easy. Either way, with the affordable price, we don’t mind the distance. And there were plenty of local shops and restaurants around the block that we could check out anyway.

That said, the hotel itself was incredible. Aside from its location, the room was great. The pictures might not do it justice, but we only have high remarks on the guestrooms. We were perfectly comfortable in our room, especially since it was equipped with a plush bed, a sofa, and a cable TV, too. If you require a cot, the hotel can provide one. Or if you have the extra budget, you can go all out for the hotel’s suite, which with a kitchen, a dining and seating area, and a fireplace. But other than that, we found our standard room to be quite ideal.

As for the services, we couldn’t be more satisfied. Other than having staff that are always attentive, we also got a free parking spot, which is super convenient in SF. However, breakfast wasn’t available at the hotel, but we were able to get a 10% discount at the nearby  Mel’s Diner and Home Plate. That’s why it was one of the best cheap hotels in San Francisco near Pier 39 for us.

The Mosser Hotel

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The Mosser Hotel is located in the heart of Union Square, home to San Francisco’s commercial hub, high-end shops, and restaurants. Yerba Buena Garden is just around the corner from the hotel, and SF MoMA was only a few minutes walk for us. In fact, the area is also teeming with museums worth visiting. And while Pier 39 is 15 minutes by car, we had no problem catching a BART to the Bay Area.

Now, The Mosser is a classic budget-friendly hotel in the city center. Meaning, we wouldn’t expect the rooms to be the most spacious. And if you really need to squeeze your spending, you can opt out of the en-suite rooms, a go for the one with shared bathrooms. That said, we got the one with an en-suite, and the in-room amenities were a cable TV, a settee, and a desk.

Overall, we got what we needed staying at The Mosser. And even though it’s a ‘budget hotel,’ the interior design was on fleek. Housed in a beautiful Victorian building, the hotel lobby is especially sleek with wood paneling and tiled floors. There was no breakfast, but there was Mel’s Drive-In a block away, for a cheap grub.

Super 8 by Wyndham San Francisco/Union Square Area

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Whenever we’re traveling, we can always rely on a Super 8 hotel to provide us with high-quality cheap accommodation. And this time we got to stay at the Super 8 by Wyndham San Francisco/Union Square Area. The cheap hotel in San Francisco near Pier 39 has many public transportation options, so getting to all the popular spots was a breeze. The ideal location also gave us plenty of dining options, from cheap halal foods to high-end cafes, and more.

That said, like many other Super 8 hotels we’ve been to, this one is also super well-maintained, clean, and has spacious rooms. We got the standard room, and it came with a private bathroom and free toiletries, a cable TV, a coffee machine, and other mod-cons. While we loved how nice and helpful the staff were, the hotel’s complimentary breakfast was definitely a winner for us. Since most cheap hotels don’t even offer breakfast options, getting one for free was especially top-tier.

Beresford Arms

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The Beresford Arms is a historical landmark in and of itself. The hotel has been standing on Post Street since the early 1900s, and still attracting guests from all over the world. Uniquely, the hotel lobby and rooms maintain a distinctive antique charm, while still having modern conveniences. And despite its historical significance and charming looks, the hotel remained budget-friendly for travelers like us.

Furthermore, Beresford Arms has been family-owned and operated since 1970, so it’s no wonder that the staff are extra hospitable. On top of that, we also get to enjoy various amenities. Starting with a complimentary European breakfast, and free snacks & drinks at social hours. Beyond that, our room was amazing. It was Victorian-inspired, with a TV, and a minibar among other mod-cons. We definitely scored ourselves a great deal staying here, especially with the Fisherman’s Wharf and Pier 39 being 15 minutes from the hotel, and public transportation was easily available.

Hotel Fiona

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While most budget-friendly near Pier 39 focus more on practicality, Hotel Fiona still made sure to remain chic and stylish, with its eclectic interior design. Stepping into the hotel, we were greeted by not only the attentive staff but also a pop of color in the lobby. The stylistic choice also extended to our room, which sported a patterned wallpaper, a colorful dresser, and most importantly, a comfy bed. We also got several mod-cons including a smart TV and a coffee maker.

Moreover, while the hotel didn’t offer breakfast, there was a coffee station with free hot beverages for us to enjoy. Plus, neighboring the hotel were several cheap dining options. Lastly, for a budget hotel, we didn’t expect to get access to a heated pool. But alas, since they’re sister hotels, we got to enjoy dipping into the rooftop pool at the SoMA Hotel across the street.

Nob Hill Hotel

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The Nob Hill area is mostly known to be historic and luxurious. But amidst the opulent neighborhood, the Nob Hill Hotel provided us with a budget-friendly option. Though, like many of the hotels in this area, the Nob Hill Hotel still sports that luxurious look and high-end hospitality. Despite the affordable price point, the staff treated us like royalty. Plus, having an on-site fitness center was a nice added facility.

Furthermore, the hotel has a mix of newly renovated room and classic Victorian rooms. We wanted to stay at the renovated one and the staff were able to help us with that. Obviously, our room was more modern, with contemporary furnishing, and mod-cons like a TV, a coffee machine, and a bathtub in the en-suite.

Lastly, like most of San Fransisco, the area is also very walkable, and we had no problem finding affordable restaurants nearby. And to reach Pier 39, a 10-minute bus ride will easily take us to the Bay Area.

FOUND Hotel Carlton, Nob Hill

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The FOUND Hotel Carlton, Nob Hill was an excellent hidden gem of a cheap hotel in San Francisco near Pier 39. With its fancy and historical brick wall outlook, people wouldn’t expect that the hotel offers budget-friendly accommodation. We were pleasantly surprised that we didn’t have to blow over our budget when we booked a room. Furthermore, the services and hospitality here were akin to any of the high-end hotels we’ve been to. The staff were professional and assisted our every need. From the moment we got to the hotel, they were quick to make us feel comfortable and helped us have a smooth check-in.

The room that we got was also excellent. Like the rest of the hotel, our room was sleek and pristinely furnished. We also got amenities including a TV, a mini-fridge, and a hairdryer in the en-suite. Beyond that, there weren’t many amenities in the hotel besides a coffee station and water/ice machine. As for dining options, we found the French pastry shop next door to be an excellent place for breakfast.

HI San Francisco Downtown Hostel

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Best value for money. When we are truly pressed for budget, we always look for hostels as an option. And luckily, we stumbled upon HI San Francisco Downtown Hostel. It’s one of the best hostels in San Francisco, so we didn’t have to worry about its quality. Suffice to say, we had so much fun staying here. For one, the hostel provided us with plenty of common room to hang out. There were even events held on some nights so we could make friends if we wanted to.

Moreover, having different options for our lodging can also be convenient, since we could adjust it to our budget. We had no problem sharing rooms with other guests, but this time we opted for a private room en-suite for convenience. Beyond that, we didn’t expect for HI San Francisco Downtown Hostel to have so many amenities. But we enjoyed the free breakfasts and having a laundromatte, and a shared kitchen was a great way to save money.

Most importantly, the hostel is located right in the heart of Union Square, with plenty of public transportation nearby. We got the Powell Train Station within walking distance, and a bus and tram station just around the block. Getting to Pier 39 was the least of our worries.

San Remo Hotel

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Most unique cheap hotel. San Remo Hotel is by far one of our favorite cheap hotels near Pier 39 San Fransisco. It’s located in North Beach, amid the city’s oldest and most popular tourist destination, with Fisherman’s Wharf and Pier 39 only four blocks away. Beyond the location, the hotel itself has so much lore. For one, the hotel is housed in a historical 1906 building and maintains its old-world charm, with vintage furnishing, and personalized knick-knacks.

Furthermore, the hotel’s unique features didn’t stop there. Each room at the hotel has a different decor, all being European-inspired, and will give you a sense of nostalgia. If you’re willing to spend extra, the hotel also offers a penthouse, which has a private rooftop terrace. That said, we opted for a standard room, which was just as comfortable. The only downside was not having an en-suite, but the staff made sure to keep the shared bathroom clean at all times.

Lastly, we only had amenities like free WiFi, a vending machine, and an ATM, but the hotel’s location and charm were obviously its main selling point. We could just easily get food at any of the neighboring restaurants. Besides, the hotel also pridefully hosts one of the oldest Italian restaurants in SF, the Fior D’Italia, which we got a chance to dine at.

Marina Motel

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Overall best. Marina Motel is an amazing hotel through and through. It has all the features we wanted. Firstly, it’s located on the bustling Lombart St in the Marina District, putting us 10 minutes from Pier 39. And with a bus stop around the corner, we had no problem getting around. Secondly, amidst the buzzing neighborhood, the Marina Motel offered us secluded accommodation with its blossoming garden, making the hotel look extra pretty.

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”If you can’t tell already, we are in love with Marina Motel’s beautiful garden. It adds a fairy-tale vibe to the hotel, giving us an unforgettable experience.”

WOW Travel

Now, when it comes to hospitality. We had nothing but good things to say. The staff made an extra effort to cater to our personal preferences and were able to get us a room in the courtyard, so we had direct access to the cobblestone courtyard garden. Our room itself was simply excellent. It was comfy, the bed was plush, and we got mod-cons including a microwave, a coffee maker, a fridge, and a TV. However, there was no breakfast option but did get a free parking spot. And for food, there were more than enough restaurants in the block for us to choose.

Overall, everything at the Marina Hotel was to our liking. There’s a reason why the hotel has been successfully running since 1930. The same family who’s been managing the hotel sure knows what they’re doing.

Our Verdict!

All of the cheap hotels in San Francisco near Pier 39 that we have on this list are guaranteed to have you leaving satisfied and with your budget intact. But among all of them, the Marina Motel just captured our hearts the most. Not only was it affordable, but the well-manicured flower garden just added to our already great experience of staying there. That said, other cheap hotels also stood out to us for their own specific feature that you might be interested in.

• Best value for money: HI San Francisco Downtown Hostel
• Best location: The Wharf Inn
• Most unique cheap hotel: San Remo Hotel

Where to Stay in San Francisco near Pier 39?

Pier 39 is one of the most famous tourist spots in San Francisco, located in the North Beach area by the water. If you want to stay within walking distance of Pier 39 and the bay, North Beach is a great starting point. However, hotels in the area can be expensive, though we managed to find a few hidden gems. Otherwise, you might go beyond your budget. The same applies to the Fisherman’s Wharf area, just a few blocks from Pier 39. It’s a prime spot with local shops and restaurants, but budget-friendly hotels can be hard to find. Still, the location is fantastic, with iconic views and attractions everywhere.

If you don’t mind a bit of distance, the Marina District is a great option. It’s close to the Wharf, and you can reach the bay in 10 minutes from Lombard Street. The area also offers sights like the Palace of Fine Arts, Fort Mason, and a lively nightlife. Furthermore, Nob Hill and Union Square, while not near the bay, are in the city center and offer a wide range of hotels, including some of our best picks for cheap hotels in San Francisco near pier 39. It’s dubbed as the commerce hub of SF, with high-rise buildings, luxurious shopping centers, and fancy bars & restaurants. There are also plenty of parks and museums in the area that are worth visiting.

Overall, with San Francisco’s accessible public transportation, it’s easy to reach Pier 39 and other iconic spots, no matter where you stay. And if you need recommendations on what to do in San Francisco, take a peek at our top things to do in San Francisco.

What time of year are the sea lions at Pier 39?

Typically the sea lions stay all year long from late summer to early spring. That said, during breeding seasons, some adult female sea lions may head south to the breeding grounds, and adult males migrate to the north. But mostly, there are a handful of juvenile sea lions that remain in the San Fransisco Bay.

What is the difference between BART and MUNI in San Francisco?

For starters, they’re both public transportation in SF. BART stands for Bay Area Rapid Transportation, and it’s basically a train system that connects the San Francisco Peninsula with communities in the East Bay and South Bay. While MUNI is a nickname for San Francisco Municipal Railway and is used to travel within San Francisco’s city limits. The service includes bus lines, trolleybuses, light rail lines, and cable cars.

How do I get to Alcatraz?

The only way to reach Alcatraz Island is by ferry, as it’s surrounded by water! Alcatraz tour tickets cover the ferry ride, access to the island, the cellhouse audio tour of the prison, and additional features.