Cheap flights from Houston to San Juan from $146

If you’re not able to fly to San Juan in January, then December is your next best option. Flight prices from Houston to San Juan during December average around $85.

The cheapest day to depart from Houston to San Juan is on a Sunday when prices can be found for as low as $506. The most expensive day to fly to San Juan is Friday, with ticket prices averaging around $571.

The cheapest time of day to fly to San Juan is at noon when flights can be purchased for as low as $394. If you have a flexible travel schedule, then try to avoid flying in the evening when prices are $541 on average. Flights to San Juan from Houston in the evening are generally more expensive because this time of day is more convenient for travelers’ schedules.

Fly from Houston George Bush Intcntl to San Juan Luis Munoz Marin Intl for the best Houston - San Juan flight prices

You are more likely to see cheaper flights to San Juan from Houston when booking weeks ahead of your departure date. In general, you can expect to find flights to San Juan for around $410 when searching weeks out. However, flight prices might be lower outside of this timeframe. For example, people recently found flights to San Juan from Houston for as low as $327 on momondo.

There are 4 cabin classes available to choose from on Houston to San Juan flights. Cabin price and availability will vary by airline so perform a search above to find the right deals for you.

Delta, Southwest, and United Airlines are the most popular carriers operating from Houston to San Juan

United Airlines, Spirit Airlines and Frontier are the top three most popular airlines that fly to San Juan from Houston according to our data. United Airlines is the first choice among our users, with 50% of people opting to fly with this airline when traveling to San Juan. Keep in mind that there are 6 different airlines that fly to San Juan on a routine basis, so you have a few additional options to choose from.

Historically, on average around 23% of flights between Houston and San Juan have experienced a delay on any given week. The average delay length over the past 12 months has been 92 minutes.

Generally, flights departing in the morning tend to experience fewer delays. Flights in the early afternoon have, in the past, seen delays more frequently in comparison.

Friday is statistically the day of the week which experiences the fewest number of delays on this flight route. Sunday has historically seen more delays on average compared to the rest of the week.

According to our data, Southwest have had the least number of delays on this route over the last 12 months; with about 23% of their flights experiencing any sort of delay.

The number of flights available between Houston and San Juan is 10 per day as of May 2026. The most frequent departure time is 3:00PM, with 39% of daily flights leaving in the afternoon.

The number of flights available between Houston and San Juan is 71 per week as of May 2026. The most frequent departure day is Sat, with 15% of weekly flights leaving on this day.