| Cheap Flights: Austin to San Juan, Puerto Rico $200 r/t [September] â Southwest Southwest has round-trip flights from Austin (AUS) to San Juan, Puerto Rico (SJU) for $200, with a connection. $98-$102 each-way. Limited availability. Flights in September. Origin/Destination reversible. Southwest doesnât charge a fee for changes, cancellations, or carry-on bags. Click for more details and booking links Cheap Flights: Austin to San Juan, Puerto Rico $200 r/t [September] â Southwest . | 