Cheap flights from Boston to San Juan from $98

If you’re not able to fly to San Juan in March, then May is your next best option. Flight prices from Boston to San Juan during May average around $285.

The cheapest day to depart from Boston to San Juan is on a Wednesday when prices can be found for as low as $326. The most expensive day to fly to San Juan is Friday, with ticket prices averaging around $359.

The cheapest time of day to fly to San Juan is in the afternoon when flights can be purchased for as low as $284. If you have a flexible travel schedule, then try to avoid flying in the morning when prices are $364 on average. Flights to San Juan from Boston in the morning are generally more expensive because this time of day is more convenient for travelers’ schedules.

Fly from Boston Logan Intl to San Juan Luis Munoz Marin Intl for the best Boston Logan Intl - San Juan flight prices

You are more likely to see cheaper flights to San Juan from Boston when booking weeks ahead of your departure date. In general, you can expect to find flights to San Juan for around $326 when searching weeks out. However, flight prices might be lower outside of this timeframe. For example, people recently found flights to San Juan from Boston for as low as $283 on momondo.

Southwest, Delta, and JetBlue are the most popular carriers operating from Boston Logan Intl to San Juan

JetBlue, Spirit Airlines and Delta are the top three most popular airlines that fly to San Juan from Boston according to our data. JetBlue is the first choice among our users, with 56% of people opting to fly with this airline when traveling to San Juan. Keep in mind that there are 7 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 25% of flights between Boston and San Juan have experienced a delay on any given week. The average delay length over the past 12 months has been 150 minutes.

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

Wednesday 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, Delta have had the least number of delays on this route over the last 12 months; with about 17% of their flights experiencing any sort of delay.

The number of flights available between Boston and San Juan is 7 per day as of May 2026. The most frequent departure time is 10:00PM, with 55% of daily flights leaving in the evening.

As of May 2026, there are 52 flights per week flying from Boston to San Juan. The most common day of the week flights depart is Fri, with 27% of flights taking off on this day.