Cheap flights from Boston to San Juan from $164

If you’re not able to fly to San Juan in March, then January is your next best option. Flight prices from Boston to San Juan during January average around $291.

The cheapest day to depart from Boston to San Juan is on a Monday when prices can be found for as low as $364. The most expensive day to fly to San Juan is Thursday, with ticket prices averaging around $399.

The cheapest time of day to fly to San Juan is in the afternoon when flights can be purchased for as low as $349. If you have a flexible travel schedule, then try to avoid flying in the morning when prices are $389 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 $344 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 $285 on momondo.

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

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

JetBlue, Delta and Frontier 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 69% 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 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 151 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.

Tuesday 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 18% of their flights experiencing any sort of delay.

The number of flights available between Boston and San Juan is 7 per day as of June 2026. The most frequent departure time is 9:00PM, with 61% of daily flights leaving in the evening.

As of June 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 25% of flights taking off on this day.