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

Return flights

19 Sep - 26 Sep	United
13 Sep - 19 Sep	Delta
18 Sep - 22 Sep	United
22 Sep - 26 Sep	United
17 Sep - 22 Sep	United
04 Sep - 10 Sep	Southwest Airlines
11 Sep - 14 Sep	Frontier Airlines
10 Sep - 16 Sep	Alaska Airlines
05 Sep - 14 Sep	Alaska 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 234€

Return flights