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

Return flights

22 Sep - 26 Sep	United	direct
06 Sep - 18 Sep	United	direct
17 Sep - 25 Sep	United	direct
26 Sep - 10 Oct	United	direct
15 Sep - 18 Sep	United
17 Sep - 20 Sep	United
07 Sep - 11 Sep	United
17 Sep - 24 Sep	United
15 Sep - 29 Sep	United
17 Sep - 01 Oct	United
20 Sep - 04 Oct	United
23 Sep - 07 Oct	United
16 Sep - 20 Sep	Southwest Airlines
18 Sep - 23 Sep	Southwest Airlines
30 Sep - 04 Oct	United
24 Sep - 08 Oct	United
25 Sep - 09 Oct	United
27 Sep - 11 Oct	United
19 Sep - 03 Oct	United	direct
14 Sep - 02 Oct	Spirit Airlines	direct

Also check the deals for one-way flights from Houston 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 Houston to San Juan in September from $156

Return flights