Cheap Flights from Jacksonville, FL to San Diego, CA from $99

On Cheapflightsplus.com you will find 1 direct and 527 connecting flights from Jacksonville to San Diego. You can compare airfare deals from 6 airlines and multiple travel sites from $99, book and save on cheap plane tickets and last minute offers. Also check out JAX-SAN flight schedule to find best flight time, convenient departure and arrival airports.

Flight Information

Below we will explain in detail what the flights cost on the destination from Jacksonville to San Diego depends on and how to choose the most interesting flight option for you.

Distance between Jacksonville and San Diego is 3355 miles. Time difference between the cities is 3h. Airplanes depart 05:36 to 21:48 from 4 Jacksonville airports and arrive 05:36 to 21:48 to 11 San Diego airports. Average flight time is 5h 5m.

  • The fastest flight 5h 5m
  • Average flight time 5h 5m
  • The earliest flight 05:36
  • The latest flight 21:48
  • Distance 2085 ml

The cheapest months to travel to San Diego are june (from 99 $), august (from 105 $), may (from 111 $).

The most expensive months are october (from 270 $), september (from 264 $), july (from 136 $).

What is the lowest airfare Jacksonville to San Diego?

The cheapest plane ticket found by our users is $99. This airfare is for economy class on one-way F92853 flight by Frontier Airlines for June 6, 2025 which leaves Jacksonville in Jacksonville at 19:29 am and arrives at San Diego San Diego at 23:48.

Economy class
$99
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Business class
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First class
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Flight Schedule Jacksonville (Florida) to San Diego (California)

09:31 — 11:36
5h 5m flight time
Find flight
from$105
Jacksonville — San Diego
MX706 Mexicana
12:57 — 16:22+1day
30h 25m flight time
Find flight
from$104
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
23h 56m stop
14:45 — 16:22 Des Moines — San Diego
G42063 Allegiant Air
12:57 — 07:13+1day
21h 16m flight time
Find flight
from$122
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
7h 32m stop
22:22 — 23:34 Des Moines — Las Vegas
G449 Allegiant Air
6h 27m stop
06:00 — 07:13 Las Vegas — San Diego
NK2502 Spirit Airlines
12:57 — 19:53+1day
33h 56m flight time
Find flight
from$122
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
7h 32m stop
22:22 — 23:34 Des Moines — Las Vegas
G449 Allegiant Air
19h 3m stop
18:36 — 19:53 Las Vegas — San Diego
NK2020 Spirit Airlines
12:57 — 23:29+1day
37h 32m flight time
Find flight
from$122
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
22h 26m stop
22:22 — 23:34 Des Moines — Las Vegas
G449 Allegiant Air
7h 54m stop
22:42 — 23:56 Las Vegas — San Diego
NK2390 Spirit Airlines
12:57 — 16:19+1day
30h 22m flight time
Find flight
from$124
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
23h 54m stop
14:43 — 16:19 Des Moines — San Diego
G4474 Allegiant Air
12:57 — 18:03+1day
32h 6m flight time
Find flight
from$128
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
7h 32m stop
22:22 — 23:34 Des Moines — Las Vegas
G449 Allegiant Air
17h 10m stop
16:43 — 18:03 Las Vegas — San Diego
NK2295 Spirit Airlines
12:57 — 16:10+1day
30h 13m flight time
Find flight
from$136
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
23h 50m stop
14:39 — 16:10 Des Moines — San Diego
G42074 Allegiant Air
12:57 — 19:53+1day
33h 56m flight time
Find flight
from$137
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
22h 32m stop
13:21 — 14:37 Des Moines — Las Vegas
G426 Allegiant Air
3h 59m stop
18:36 — 19:53 Las Vegas — San Diego
NK2020 Spirit Airlines
12:57 — 23:56+1day
37h 59m flight time
Find flight
from$137
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
22h 32m stop
13:21 — 14:37 Des Moines — Las Vegas
G426 Allegiant Air
8h 5m stop
22:42 — 23:56 Las Vegas — San Diego
NK2390 Spirit Airlines
12:57 — 09:55+1day
23h 58m flight time
Find flight
from$141
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
7h 42m stop
22:31 — 23:37 Des Moines — Las Vegas
G415 Allegiant Air
9h 3m stop
08:40 — 09:55 Las Vegas — San Diego
NK1154 Spirit Airlines
12:57 — 17:55+1day
31h 58m flight time
Find flight
from$141
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
7h 42m stop
22:31 — 23:37 Des Moines — Las Vegas
G415 Allegiant Air
17h 1m stop
16:38 — 17:55 Las Vegas — San Diego
NK1150 Spirit Airlines
12:57 — 23:00+1day
37h 3m flight time
Find flight
from$141
12:57 — 14:49 Jacksonville — Des Moines
G43451 Allegiant Air
7h 42m stop
22:31 — 23:37 Des Moines — Las Vegas
G415 Allegiant Air
22h 9m stop
21:46 — 23:00 Las Vegas — San Diego
NK1152 Spirit Airlines
19:22 — 00:11+1day
7h 49m flight time
Find flight
from$111
19:22 — 21:30 Jacksonville — Dallas
F92853 Frontier Airlines
1h 18m stop
22:48 — 00:11 Dallas — San Diego
F91769 Frontier Airlines
19:29 — 23:48
7h 19m flight time
Find flight
from$99
19:29 — 21:27 Jacksonville — Dallas
F92853 Frontier Airlines
1h 13m stop
22:40 — 23:48 Dallas — San Diego
F91425 Frontier Airlines
Full flight schedule will help you in detecting at what time planes fly from Jacksonville to San Diego. You can also specify the concrete flights and airlines on the route and how long the flight actually is. Use the calendar for today, tomorrow or other specific date as some flights are available only on certain days of the week.
*Departure and arrival times - local. Updated on December 14, 2025.

Popular Airlines on the Route

The flight Jacksonville — San Diego is served by 6 regular airlines and 3 low-cost airlines. Most of the flights on this route are operated by Alaska Airlines - 79 departures per week at the price of from $ 270 . And the most expensive tickets are offered by United Airlines airline - from $ 866.

Direct flights

There are 1 nonstop flights on the route. The fastest direct flight is MX706 by Mexicana takes 5h 5m and the cheapest is F92853 by Frontier Airlines for $105.

  • MX - Mexicana
    from $105
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Connecting Flights

There are 527 flights with layovers on the route. The fastest connecting flight is UA2453 by United Airlines takes 6h 27m and the cheapest is F92853 by Frontier Airlines for $99.

  • AS - Alaska Airlines
    from $270
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  • F9 - Frontier Airlines
    from $99
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  • SY - Sun Country Airlines
    from $177
    Find
  • MX - Mexicana
    from $256
    Find
  • UA - United Airlines
    from $271
    Find
  • G4 - Allegiant Air
    from $104
    Find
See more connecting flights

Airports

You can fly from Jacksonville to San Diego from 4 airports (Jacksonville, Craig Municipal, Jacksonville NAS, Cecil Field).

Jacksonville airports

  • Jacksonville-JAX
    from $99
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  • Craig Municipal-CRG
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  • Jacksonville NAS-NIP
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  • Cecil Field-VQQ
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San Diego airports

  • San Diego-SAN
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  • San Diego Regional-USA
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  • Gillespie Field-SEE
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  • Golden Triangle Reg.-GTR
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  • El Cajon-CJN
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  • Lowndes County-UBS
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  • Miramar NAS-NKX
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  • Montgomery Field-MYF
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  • North Island NAS-NZY
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  • Brown Field Municipal-SDM
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  • AFB-CBM
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How to book a plane ticket yourself?

How to book an air ticket yourself?
  • Fill in the search parameters — cities of departure and destination, departure and return dates and click «Find flights»
  • Select the best flight that you like. Please, check the airports of departure and arrival. Select the best fare, but pay attention to the following flight details - airports of departure and arrival, flight duration and layovers. Please use filters and sort to find the best flight.
  • Click «Buy» when you are ready — our system will redirect you to the site that sells the selected flight ticket.
  • Fill in all passenger and payment information — passport and contact information, please double check all passengers’ names and make a payment for your itinerary.
  • That's it — you will receive an email with your e-ticket usually within 10 minutes after your flight is confirmed. Please, print the e-ticket and have it with you at the airport. You would need to have only a passport and/or a required form of ID to travel. Please, check your Visa requirements if you travel outside of the United States or Canada.

    To find a plane ticket, please select dates.

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