Find Boutique Hotels in Mission Valley, CA
Change your mindBook hotels with free cancellation
Be pickySearch almost a million properties worldwide
Check availability on Mission Valley Boutique Hotels
Our top choices for Mission Valley boutique hotels
Alma San Diego Downtown, a Tribute Portfolio Hotel
Alma San Diego Downtown, a Tribute Portfolio HotelDowntown San Diego
9.0 out of 10, Wonderful, (881)
"Friendly staff throughout stay and clean rooms"
Alvin
The price is NT$3,395
NT$5,212 total
includes taxes & fees
Jan 4 - 2026/1/5
8.6 out of 10, Excellent, (1475)
"I loved my stay here"
José
Hotel Republic San Diego, Autograph Collection
Hotel Republic San Diego, Autograph CollectionDowntown San Diego
9.0 out of 10, Wonderful, (1200)
"Modern decor, great restaurant, convenient to all attractions in San Diego."
Nelson
The price is NT$5,627
NT$7,982 total
includes taxes & fees
Dec 30 - Dec 31
Hotel Indigo San Diego-Gaslamp Quarter by IHG
Hotel Indigo San Diego-Gaslamp Quarter by IHGDowntown San Diego
8.8 out of 10, Excellent, (1008)
"Room was clean and well-appointed. Proximity to Petco Park and downtown area was perfect"
Jennifer
The price is NT$4,527
NT$6,414 total
includes taxes & fees
Jan 4 - 2026/1/5
9.6 out of 10, Exceptional, (1007)
"The best hotel ever "
oleg
The price is NT$6,238
NT$7,171 total
includes taxes & fees
Jan 21 - 2026/1/22
8.6 out of 10, Excellent, (1339)
"Nice breakfast "
Marcos
The price is NT$2,644
NT$2,913 total
includes taxes & fees
Dec 30 - Dec 31
9.0 out of 10, Wonderful, (1005)
"Everything about the Hotel including staff was fantastic"
Donna
The price is NT$5,050
NT$6,948 total
includes taxes & fees
Jan 1 - 2026/1/2
8.6 out of 10, Excellent, (1004)
"Lovely spot would stay again "
danixa
The price is NT$3,607
NT$4,074 total
includes taxes & fees
Jan 5 - 2026/1/6
Lowest nightly price found within the past 24 hours based on a 1 night stay for 2 adults. Prices and availability subject to change. Additional terms may apply.
Top Mission Valley Hotel Reviews
The Atwood Hotel San Diego - SeaWorld/Zoo
10/10 Excellent
Bay Club Hotel & Marina
10/10 Excellent
Frequently asked questions
Explore a world of travel with Expedia
- Family Hotels in Downtown San Diego
- Historic Hotels in Old Town San Diego
- Gay friendly Hotels in San Diego
- Family Hotels in San Diego
- Hotels with a Pool in Downtown San Diego
- Pet-Friendly Hotels in San Diego County
- Ranches in San Diego County
- La Quinta Inn & Suites Hotels in Old Town San Diego
- Business Hotels in San Diego
- San Diego Hotels
- Linda Vista Hotels
- Hotels near Fashion Valley Mall
- Pet-Friendly Hotels in Old Town San Diego
- Pet-Friendly Hotels in La Jolla
- Pet-Friendly Hotels in Mission Valley
- Hillcrest Hotels
- Hotels near San Diego Zoo
- All-Inclusive Hotel Hotels in San Diego County
- 5 Star Hotels in Little Italy
- Golf Hotels in San Diego
- Pet-Friendly Hotels in North Park
- Little Italy Hotels
- Hotels near El Campo Santo
- Hotels near Old Town San Diego State Park
- Romantic Hotels in San Diego County
- Casino Hotels in San Diego
- Resorts & Hotels with Spas in Downtown San Diego
- Luxury Hotels in Mission Valley
- Casino Hotels in Midway-Pacific Highway
- Hostels in San Diego
- Gay friendly Hotels in Downtown San Diego
- Wyndham Hotels in Hillcrest
- Waterpark Hotels in San Diego
- Hotels with Bars in North Park
- Gay friendly Hotels in San Diego County
- Family Hotels in Midway-Pacific Highway
- Casino Hotels in Mission Valley
- Beach Hotels in Gaslamp Quarter
- Gay friendly Hotels in North Park
- Hotels with Free Parking in Gaslamp Quarter
- Resorts & Hotels with Spas in San Diego
- Hotels near Rio Vista Station
- Romantic Hotels in Old Town San Diego
- Hotels with Bars in San Diego
- Flights from Lincoln (LNK) to San Diego (SAN)
- Flights from Tokyo (HND) to San Diego (SAN)
- Flights from Taipei (TPE) to San Diego (SAN)
- Flights from Warsaw (WAW) to San Diego (SAN)
- Flights from Kenmore (KEH) to San Diego (SAN)
- Flights from Fort Leonard Wood (TBN) to San Diego (SAN)
- Flights from Kansas City (MCI) to San Diego (SAN)
- Klm London (LHR) to San Diego (SAN) flights
- Flights from Chicago (MDW) to San Diego (SAN)
- Delta Minneapolis (MSP) to San Diego (SAN) flights
- Flights from Tijuana (TIJ) to San Diego (SAN)
- Flights from Thunder Bay (YQT) to San Diego (SAN)
- Flights from Vaeroy (VRY) to San Diego (SAN)
- Flights from San Francisco (SFO) to San Diego (MYF)
- Flights from Gwadar (GWD) to San Diego (SAN)
- Flights from Cincinnati (LUK) to San Diego (SAN)
- Flights from Bemidji (BJI) to San Diego (SAN)
- Alaska Airlines Boise (BOI) to San Diego (SAN) flights
- Flights from Lome (LFW) to San Diego (SAN)
- Flights from Kahului (OGG) to San Diego (SAN)
- Flights from College Station (CLL) to San Diego (SAN)
- United Newark Liberty Intl. Airport (EWR) to San Diego (SAN) flights
- Delta Madrid (MAD) to San Diego (SAN) flights
- Flights from Chattanooga (CHA) to San Diego (SAN)
- Delta Boston (BOS) to San Diego (SAN) flights
- Flights from Toyama (TOY) to San Diego (SAN)
- Flights from Syracuse (SYR) to San Diego (SAN)
- Flights from San José del Cabo (SJD) to San Diego (SAN)
- Flights from Lihue (LIH) to San Diego (SAN)
- Flights from Tunis (TUN) to San Diego (SAN)
- Japan Airlines Shanghai (SHA) to San Diego (SAN) flights
- Flights from Pittsburgh (PIT) to San Diego (SAN)
- United Amsterdam (AMS) to San Diego (SAN) flights
- Flights from Williams Lake (YWL) to San Diego (SAN)
- Flights from Tokyo (NRT) to San Diego (SAN)
- Flights from Fresno (FAT) to San Diego (SAN)
- Flights from Chicago (ORD) to San Diego (SAN)
- Flights from Augusta (AGS) to San Diego (SAN)
- Hertz Rental Cars in San Diego
- Enterprise Rental Cars in Little Italy
- Car rentals near North Park
- Car rentals near Mo'olelo Performing Arts Company
- Economy Rent a Car Rental Cars in Little Italy
- Car rentals near Red Spade Theater
- Avis Rental Cars in Downtown San Diego
- Enterprise Rental Cars in Mission Valley
- Sixt Rental Cars in Mission Valley