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

Return flights

25 Sep - 29 Sep	United
13 Sep - 17 Sep	United
05 Sep - 12 Sep	United
19 Sep - 26 Sep	United
20 Sep - 04 Oct	Delta
12 Sep - 17 Sep	United
12 Sep - 20 Sep	United
01 Sep - 07 Sep	United
02 Sep - 07 Sep	United
11 Sep - 16 Sep	Southwest Airlines
05 Sep - 15 Sep	Alaska 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 298€

Return flights