Guide
San Juan airport delays: how reliable is flying out of SJU?
Flights from San Juan to the mainland ran 77.7% on time over September 2025 to August 2026. The cancellations came in the mainland winter, not in hurricane season.
Nearly every airliner that leaves San Juan for the mainland got there from the mainland, after a flight of 1,000 to 2,000 miles over open water. That single fact explains more about Luis Muñoz Marín International than its weather, its runways or its airlines.
It is the lens I would read everything else here through. Late-arriving aircraft account for 52% of San Juan's delay minutes, one of the highest shares of any airport on this site and far above the national 40%.
Because Puerto Rico is a US territory, its flights to the mainland are domestic in the DOT's data, reported and scored like any flight from Boston to Chicago. Over September 2025 to August 2026, 77.7% of the 35,332 scheduled departures from San Juan arrived on time, rank 35 of 60 airports and just below the national 77.3%. 2.11% of flights were cancelled, against 1.89% nationally, and 7.9% arrived an hour or more late.
A borrowed delay, not a local one
The air traffic system accounts for only 12% of San Juan's delay minutes, one of the lowest shares in the country; extreme weather accounts for 1%. San Juan's own airspace is rarely the problem. The airline's own causes and, above all, aircraft that turned up late from New York, Orlando or Philadelphia make up most of it.
Share of all delay minutes. Darker is a bigger share. Air traffic is the National Airspace System category; weather is extreme weather only.
| Late aircraft | Airline | Air traffic | Weather | |
|---|---|---|---|---|
| SJU | 52 | 35 | 12 | 1 |
| US | 40 | 33 | 21 | 6 |
Shares of delay minutes reported by the airlines. Source: US DOT Bureau of Transportation Statistics, September 2025 to August 2026.
That shows up clearly in the two directions of each route, which the pipeline keeps as separate records. The flight to San Juan leaves a congested mainland airport and picks up delay there; the flight back leaves an uncongested one but inherits whatever the inbound brought. On balance the southbound leg is the worse one. JFK to San Juan ran 70.2% on time against 77.8% for San Juan to JFK. Philadelphia to San Juan managed 63.3%, rank 2,928 of 2,978 routes. The opposite-direction guide explains why the same aircraft can run so differently each way.
US average 77.3%
55.0%80.0%
For comparison with the departures from San Juan further down. Dashed line: US average. Source: US DOT Bureau of Transportation Statistics, September 2025 to August 2026.
JetBlue's island, with Delta and United out in front
JetBlue at San Juan flies about a third of the departures, more than any other airline. American, Frontier, Southwest, Delta, United and Spirit split the rest.
SJU average 77.7%
60.0%90.0%
Departures from SJU. The dashed line is the airport average. Source: US DOT Bureau of Transportation Statistics, September 2025 to August 2026.
In this period Delta and United led San Juan, each flying mainly to its own hubs. JetBlue sat below the airport average, and Frontier and Spirit trailed; Spirit also cancelled more than any other carrier at SJU, and its figure covers less of the year than the others: Spirit's filings stop in early May 2026, and there are no Spirit flights in the data for June or July. The gaps are widest on shared routes. Delta on San Juan to Atlanta ran far ahead of Frontier on the same route, and on the New York run Delta's San Juan to JFK beat JetBlue's by a wide margin. The low-cost carriers guide explains why thin spare-aircraft cover hurts most on long, isolated routes like these.
The morning bank is the one to book
Departures between 5am and 8am ran 89.2% on time. After that the curve settles into the low seventies: 72.0% in the 2pm to 5pm window, 71.7% between 5pm and 8pm. The 17.5-point gap between dawn and evening is smaller than the national 21.3, consistent with afternoon departures that are not piling up local delay so much as carrying mainland delay, which can arrive at any hour.
The dawn flights are the ones that spent the night on the island. United 1644 to Houston, Delta 1763 to Atlanta and Delta 1854 to JFK all leave between 7am and 7:30am and rank among the most punctual flight numbers from San Juan. At the other end, Frontier 2871, a late-afternoon departure to Atlanta, was on time barely half the time.
Hurricane season was not the problem this year
Figures are on-time percentages. Darkest column is the best, lightest the worst. Source: US DOT Bureau of Transportation Statistics, September 2025 to August 2026.
The weakest months were August 2025 at 74.0% and July 2026 at 71.5%, both peak summer travel months. The best were May 2026 at 84.7% and June 2026 at 83.1%. September 2025, the heart of the hurricane season, ran 80.7% and cancelled almost nothing, on a schedule trimmed to its lowest level of the year.
The cancellations came from the north. January 2026 had the worst cancellation rate of the year by a distance, spread across the routes to New York, Boston, Philadelphia, Chicago and Dallas: the aircraft could not get out of storm-hit mainland airports to fly the return. January 2026 had the year's highest national cancellation rate, and it was concentrated at Charlotte, Dallas-Fort Worth and Washington National rather than in the snow belt, so a southern hub is not automatically the safe way home that month. February 2026 followed. The on-time rate in both months, 73.3% and 74.7%, was below the airport's average as well.
One year of data is one sample, and this one contained no direct hurricane strike on Puerto Rico. When one does hit, it does not produce a bad on-time month; it closes the airport for days, as Maria did in 2017, and no booking choice avoids it.
Weekdays matter less. Wednesday departures ran 80.8% and Sunday 73.8%, the airport's worst day.
The routes out of San Juan
US average 77.3%
60.0%95.0%
The line under each bar is the route's cancellation rate. Dashed line: US average. Source: US DOT Bureau of Transportation Statistics, September 2025 to August 2026.
The busiest route, San Juan to Orlando, ran 78.0% and cancelled only 1.21%, with Southwest the most punctual of its four airlines. The best big routes run to legacy hubs: San Juan to Houston at 88.7%, to Charlotte at 86.0% and to Atlanta at 81.6%. The weakest end in the Northeast: San Juan to Hartford at 69.8%, to Boston at 70.8% and to Philadelphia at 71.9%, which also cancelled 3.61% of its flights. Those are the routes a winter storm stops.
What I would book out of San Juan
Fly the first departure. A morning flight leaves on an aircraft that has been on the ground in San Juan all night, which removes the island's biggest single source of delay.
Pick the airline before the route. Delta and United out of San Juan ran well ahead of the low-cost carriers on the same city pairs. Given the choice on the Atlanta route, I would not pick the late-afternoon Frontier flight over Delta's morning one. If you are going to Atlanta, New York or Chicago, the legacy option was the reliable one in this period.
For the Northeast between December and March, keep a spare day. San Juan's weather is not the risk; the destination's is. A cancelled flight to Boston or Philadelphia in a snowstorm may not have an empty seat for two or three days, because every flight back is full of the people who were due to fly the day before. The winter storm guide covers the mainland end.
Coming to Puerto Rico, expect more delay than going home. The southbound flights ran worse than the northbound ones on every big route in this period. Leave margin for a cruise departure or a same-day inter-island connection.
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