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Cheap Flights from San Diego to San Juan

Compare San Diego to San Juan flight deals

Find the cheapest month or even day of the year to fly to San Juan

Book the best San Juan fare with no extra fees

Flight deals from San Diego to San Juan

Looking for a cheap last-minute deal or the best return flight from San Diego to San Juan? If you want to travel next month, return fares start from R 5,895. Find the lowest prices on one-way and return tickets right here.
San Juan.R 2,499 per passenger.Departing Wed, 30 Sep.One-way flight with Delta.Outbound indirect flight with Delta, departs from San Diego International on Wed, 30 Sep, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 2,499, select.
San Juan.R 2,991 per passenger.Departing Sun, 23 Aug.One-way flight with Frontier Airlines.Outbound indirect flight with Frontier Airlines, departs from San Diego International on Sun, 23 Aug, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 2,991, select.
San Juan.R 3,191 per passenger.Departing Sat, 16 Jan.One-way flight with United.Outbound indirect flight with United, departs from San Diego International on Sat, 16 Jan, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,191, select.
San Juan.R 3,196 per passenger.Departing Tue, 20 Oct.One-way flight with Southwest Airlines.Outbound indirect flight with Southwest Airlines, departs from San Diego International on Tue, 20 Oct, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,196, select.
San Juan.R 3,197 per passenger.Departing Mon, 5 Apr.One-way flight with Delta.Outbound indirect flight with Delta, departs from San Diego International on Mon, 5 Apr, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,197, select.
San Juan.R 3,199 per passenger.Departing Mon, 31 May.One-way flight with United.Outbound indirect flight with United, departs from San Diego International on Mon, 31 May, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,199, select.
San Juan.R 3,199 per passenger.Departing Thu, 31 Dec.One-way flight with United.Outbound indirect flight with United, departs from San Diego International on Thu, 31 Dec, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,199, select.
San Juan.R 3,355 per passenger.Departing Sun, 1 Nov.One-way flight with Southwest Airlines.Outbound indirect flight with Southwest Airlines, departs from San Diego International on Sun, 1 Nov, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,355, select.
San Juan.R 3,356 per passenger.Departing Wed, 3 Mar.One-way flight with United.Outbound indirect flight with United, departs from San Diego International on Wed, 3 Mar, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 3,356, select.
San Juan.R 4,247 per passenger.Departing Wed, 29 Jul.One-way flight with Frontier Airlines.Outbound indirect flight with Frontier Airlines, departs from San Diego International on Wed, 29 Jul, arriving in San Juan Luis Munoz Marin.Price includes taxes and charges.From R 4,247, select.

Find the cheapest month to fly from San Diego to San Juan

We’re always keeping an eye on fares, so you can find the best one in seconds. It looks like San Diego to San Juan flights are currently cheapest in September.
Jul
from R 4,247
Aug
from R 2,991
Sep
from R 2,499
Oct
from R 3,196
Nov
from R 3,355
Dec
from R 3,199
Jan
from R 3,191
Feb
Find prices
Mar
from R 3,356
Apr
from R 3,197
May
from R 3,199
Jun
Find prices

Alternative San Diego to San Juan routes

Looking for the cheapest, fastest or easiest route from San Diego to San Juan? You could fly into the following airports instead.

San Juan Isla Grande

1km from central San Juan
Closest
Search flights

San Juan Luis Munoz Marin

11km from central San Juan
Cheapest
from R 2,499
Search flights

Roosevelt Roads

55km from central San Juan
Search flights

Ponce

70km from central San Juan
from R 9,292
Search flights

Vieques

82km from central San Juan
Search flights

Culebra

85km from central San Juan
from R 5,834
Search flights

San Diego to San Juan: Flight information

The things to know before you go.
Cheapest flight foundR 2,499
Cheapest month to flySeptember

Finding cheap flights from San Diego to San Juan: Frequently asked questions

There are 6 airports in San Juan: San Juan Isla Grande, San Juan Luis Munoz Marin, Roosevelt Roads, Ponce, Vieques, and Culebra.
The best price we found for a return flight from San Diego to San Juan is R 4,993. This is an estimate based on information collected from different airlines and travel providers over the last 4 days and is subject to change and availability.
Currently, there are no airlines that fly direct from San Diego to San Juan. But we found flights with one or more stops from R 4,993.
As of July 2026, there are no flights flying from San Diego to San Juan.
The cheapest month to fly from San Diego to San Juan is usually September.
If you're flying from San Diego, the cheapest airport near San Juan is San Juan Luis Munoz Marin – which is 11.3 km away from the centre of San Juan. We've found flights into this airport from R 4,993.
After crunching the numbers on our flight calendar, we found that it is currently cheapest to fly from San Diego to San Juan on Tuesday, 29 September 2026.
No airlines currently offer direct flights between San Diego and San Juan. Most routes have one or more stops.
We show every price from over 1,200 airlines and travel agents, comparing them all so you don’t have to. If you know you want to fly to San Juan but you’re not ready to book, set up a Price Alert. We’ll track prices for you, and let you know when they rise or fall.

We crunched all the numbers in our flight calendar and it looks like the cheapest time to book a flight to San Juan is around 40 days in advance, so don’t leave your flight to the last minute.

In July, the average temperature is usually around 27°C. August is typically the warmest month in San Juan, when it usually averages around 29°C. You can expect the least rain in February. The coldest month is January, with temperatures averaging 23°C. The rainiest month is September.
The cheapest airline that flies to San Juan is Delta .

Travelling from San Diego to San Juan: what you need to know

  • San Diego International Airport (SAN) is San Diego's main airport. Explore your options for booking a flight from San Diego to San Juan leaving from here.

  • Touch down at San Juan Luis Munoz Marin Airport (SJU), the chief entry point to San Juan.

  • San Juan is four hours ahead of San Diego and follows the UTC-4 timezone.

  • For a stress-free journey, arrive at the airport two hours ahead of international flights and an hour before domestic departures. This leaves you with plenty of time to board your San Diego to San Juan flight.

  • During popular months such as August, it's best to get to the airport even earlier. Plan to arrive two hours before domestic departures and four hours ahead of international flights when you fly during high season in general.

How to find the cheapest flights from San Diego to San Juan

  • Don't wait until the last minute. You're more likely to find cheap San Diego to San Juan flights if you book in advance. Airlines often offer some amazing early bird discounts.

  • The 'Whole month' tool will show you the cheapest plane tickets from San Diego to San Juan throughout the month. It's a great way to find a bargain if your plans are flexible.

  • Snapping up a cheap flight from San Diego to San Juan is a piece of cake with Price Alerts. Simply create one of these automatic alerts and we'll get in touch as soon as a better deal is available.

  • Choose your preferred arrival and departure times, number of stops and airlines by using the filters. Alternatively, sort your San Diego to San Juan flight results by 'Fastest,' 'Best' or 'Cheapest.'

Flying from San Diego

San Diego International Airport (SAN)

  • We make it a breeze to book a San Diego to San Juan flight with a stopover. To see all the options departing from San Diego International Airport, deselect 'Direct flights only.' Next, select a flight offering a stop long enough to tour the city of your choice. Some popular stopovers include:

    • Atlanta Hartsfield-Jackson Airport (ATL)

    • Dallas Fort Worth International Airport (DFW)

    • Houston George Bush Intercntl. Airport (IAH)

  • SAN is about 5 kilometres from central San Diego. If you're ride-sharing, catching a taxi or driving from the centre, it'll take 15 minutes or so to get there, depending on the traffic. If you're planning to take public transport, expect the journey time to be around 25 minutes.

  • Want a hassle-free start to your travels? Stay near San Diego International Airport. Whether you have an early flight from San Diego to San Juan or want to avoid feeling rushed, these hotels are ideal:

  • 74% of flights departing from San Diego International Airport reach their destination on schedule.

  • SAN is located at N Harbour Dr.

Arriving in San Juan

San Juan Luis Munoz Marin Airport (SJU)

  • San Juan Luis Munoz Marin Airport (SJU) to central San Juan takes about 20 minutes to reach by car. The centre is roughly 11 kilometres away.

  • When travelling by public transport, expect a journey time of roughly 1 hour.

  • If you have a late flight from San Diego to San Juan, few things beat the convenience of staying near the terminal. Grab your luggage from the carousel and then be showered and relaxing soon after at one of these hotels near SJU:

  • Explore without limits with a San Juan Luis Munoz Marin Airport rental car. Pick up your wheels from Sixt, Ace Rent a Car or U-Save and experience more of San Juan and beyond.

  • For the best deal, book your vehicle from San Juan Luis Munoz Marin Airport about two weeks in advance of your San Diego to San Juan flight.

San Juan Isla Grande Airport (SIG)

Best time to go to San Juan

  • July is the most popular month for flights from San Diego to San Juan. To steer clear of the crowds, go to San Juan in March.

  • Book a San Diego to San Juan ticket departing in August if you want to visit the city during its warmest month. You can expect temperatures in San Juan to range from 24ºC (75ºF) to 32ºC (90ºF).

  • For cooler conditions, look for a cheap flight from San Diego to San Juan in February when temperatures average between 21ºC (70ºF) and 28ºC (82ºF).

More about San Juan

  • When it comes to searching for somewhere to rest your head, you'll find the top stays in San Juan right here. Browse these hotels as soon as you've locked in your flight from San Diego to San Juan:

  • Every great holiday has to include some sightseeing. Balneario El Escambron, La Garita del morro de san juan bahia and Beach San Juan are essential stops on your San Juan itinerary.

Explore more of Puerto Rico

  • San Juan will leave a lasting impression, but there are so many other corners of Puerto Rico waiting to be explored. Around 13 kilometres southwest of San Juan, a visit to Bayamon will keep you busy. Start with leading sights like Ron del Barrilito - Hacienda Santa Ana, Parque de las Ciencias by Toroverde Power by Claro and Parque Recreativo Río Bayamón.

  • If you're looking to explore another corner of Puerto Rico, head for Carolina, about 18 kilometres southeast of San Juan. Isla Verde Beach, Carolina Public Beach and Balneario Isla Verde are among the biggest draws.

More travel options

Plan the rest of your trip from San Diego to San Juan

Prices shown on this page are estimated lowest prices only. Found in the last 12 days.