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 - 06 Oct	Spirit Airlines
25 Sep - 27 Sep	Spirit Airlines
22 Sep - 29 Sep	Frontier Airlines
19 Sep - 22 Sep	Frontier Airlines
19 Sep - 21 Sep	Frontier Airlines
21 Sep - 28 Sep	Frontier Airlines
22 Sep - 28 Sep	United
18 Sep - 22 Sep	United

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 $412

Return flights