Cheap flights from San Diego to Japan from $407

The month of February is, on average, the cheapest month to fly to Japan from San Diego, with most prices found around $901. If you aren’t able to travel to Japan during the month of February, then flying in January is also cheap. Prices for this month can be found on momondo for an average of $936.

On average, the least expensive day to fly to Japan from San Diego is on a Thursday. momondo users have found tickets for Thursday departures for as low as $1,224. However, this price may fluctuate depending on the airline, the season, and holidays. Flights from San Diego to Japan on a Friday will generally be more expensive and average around $1,498. Keep in mind that these prices on both days could fluctuate depending on the season and the demand.

Flying to Japan from San Diego at noon is the least expensive time of day to depart. momondo users have found prices as low as $1,278 when looking at flights departing at noon. In the morning is when there is more demand to fly to Japan, so prices are often more expensive at around $1,311 per ticket.

Fly from San Diego to Tokyo Narita for the best San Diego - Japan flight prices

You are more likely to see cheaper flights to Japan from San Diego when booking weeks ahead of your departure date. In general, you can expect to find flights to Japan for around $1,292 when searching weeks out. However, flight prices might be lower outside of this timeframe. For example, people recently found flights to Japan from San Diego for as low as $988 on momondo.

There are 3 cabin classes available to choose from on San Diego to Japan flights. Cabin price and availability will vary by airline so perform a search above to find the right deals for you.

Japan Airlines, Delta, and ANA are the most popular carriers operating from San Diego to Japan

Japan Airlines, ANA and United Airlines are the top three most popular airlines that fly to Japan from San Diego according to our data. Japan Airlines is the first choice among our users, with 38% of people opting to fly with this airline when traveling to Japan. Keep in mind that there are 10 different airlines that fly to Japan on a routine basis, so you have a few additional options to choose from.

Historically, on average around 32% of flights between San Diego and Japan have experienced a delay on any given week. The average delay length over the past 12 months has been 116 minutes.

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

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

According to our data, Japan Airlines have had the least number of delays on this route over the last 12 months; with about 32% of their flights experiencing any sort of delay.

The number of flights available between San Diego and Japan is 2 per day as of October 2026. The most frequent departure time is 1:00PM, with 100% of daily flights leaving in the afternoon.

As of October 2026, 16 flights take off from San Diego and land in Japan each week. The most common flight departure day for this route is Wed, with 25% of weekly flights taking off on this day.