AirHint found the following cheapest return flights from San Diego (SAN) to San Juan (SJU) in September 2025 (see full year).

Return flights

23 Sep - 30 Sep	United
22 Sep - 28 Sep	United
21 Sep - 26 Sep	United
27 Sep - 07 Oct	United
19 Sep - 26 Sep	United
06 Sep - 18 Sep	Spirit Airlines
18 Sep - 22 Sep	United
15 Sep - 22 Sep	United
03 Sep - 09 Sep	Frontier Airlines
11 Sep - 16 Sep	Spirit Airlines
03 Sep - 07 Sep	Frontier Airlines

Also check the deals for one-way flights from San Diego to San Juan in September.

The deals are updated regularly. The prices may go up as tickets are purchased by other travellers. Only the cheapest flights are offered. Select a price to book and secure these cheap prices.

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Cheapest return flights from San Diego to San Juan in September from 236€

Return flights