Cheap flights from San Francisco Bay Area to San Diego from $42

If you are unable to visit San Diego during the month of July, then departing from San Francisco Bay Area during the month June is also very affordable. Most momondo users find prices during this month for around $146.

The cheapest day to depart from San Francisco Bay Area to San Diego is on a Tuesday. Travelers who choose to depart for San Diego on a Tuesday will often find tickets for as low as $160. If your travel schedule is flexible, try to avoid departing on a Friday because tickets tend to average around $207. These prices are subject to change though, so be sure to set up a Price Alert for flights to San Diego.

The cheapest time of day to fly to San Diego is in the morning when flights can be purchased for as low as $177. Flights in the afternoon are often more expensive with an average ticket price of $199.

Fly from San Francisco to San Diego for the best San Francisco Bay Area - San Diego flight prices

You are more likely to see cheaper flights to San Diego from San Francisco Bay Area when booking weeks ahead of your departure date. In general, you can expect to find flights to San Diego for around $175 when searching weeks out. However, flight prices might be lower outside of this timeframe. For example, people recently found flights to San Diego from San Francisco Bay Area for as low as $124 on momondo.

There are 4 cabin classes available to choose from on San Francisco Bay Area to San Diego flights. Cabin price and availability will vary by airline so perform a search above to find the right deals for you.

Alaska Airlines, Southwest, and United Airlines are the most popular carriers operating from San Francisco Bay Area to San Diego

Alaska Airlines, Southwest and United Airlines are the top three most popular airlines that fly to San Diego from San Francisco Bay Area according to our data. Alaska Airlines is the first choice among our users, with 32% of people opting to fly with this airline when traveling to San Diego. Keep in mind that there are 10 different airlines that fly to San Diego on a routine basis, so you have a few additional options to choose from.

66 flights are operational daily from San Francisco Bay Area to San Diego as of March 2026. The most popular departure time for this route is 10:00AM, with 40% of flights per day taking off at noon.

466 flights are operational weekly from San Francisco Bay Area to San Diego as of March 2026. The most popular departure day for this route is Mon, with 22% of flights per week taking off on this day.