Cheap flights from San Francisco to San Diego from $63

If you are unable to visit San Diego during the month of July, then departing from San Francisco during the month June is also very affordable. Most momondo users find prices during this month for around $152.

The cheapest day to depart from San Francisco to San Diego is on a Saturday. Travelers who choose to depart for San Diego on a Saturday will often find tickets for as low as $189. If your travel schedule is flexible, try to avoid departing on a Sunday because tickets tend to average around $227. 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 $198. Flights in the afternoon are often more expensive with an average ticket price of $243.

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

You are more likely to see cheaper flights to San Diego from San Francisco when booking weeks ahead of your departure date. In general, you can expect to find flights to San Diego for around $196 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 for as low as $127 on momondo.

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

Alaska Airlines, Southwest and United Airlines are the top three most popular airlines that fly to San Diego from San Francisco according to our data. Alaska Airlines is the first choice among our users, with 33% of people opting to fly with this airline when traveling to San Diego. Keep in mind that there are 9 different airlines that fly to San Diego on a routine basis, so you have a few additional options to choose from.

Historically, on average around 21% of flights between San Francisco and San Diego have experienced a delay on any given week. The average delay length over the past 12 months has been 117 minutes.

Generally, flights departing in the morning tend to experience fewer delays. Flights in the evening have, in the past, seen delays more frequently in comparison.

Saturday is statistically the day of the week which experiences the fewest number of delays on this flight route. Friday has historically seen more delays on average compared to the rest of the week.

According to our data, United Airlines have had the least number of delays on this route over the last 12 months; with about 16% of their flights experiencing any sort of delay.

The number of flights available between San Francisco and San Diego is 54 per day as of May 2026. The most frequent departure time is 6:00PM, with 39% of daily flights leaving at noon.

As of May 2026, there are 383 flights per week flying from San Francisco to San Diego. The most common day of the week flights depart is Mon, with 17% of flights taking off on this day.