Cheap Flights from Panama City to San Juan

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Flight deals from Panama City to San Juan

Looking for a cheap last-minute deal or the best return flight from Panama City to San Juan? Find the lowest prices on one-way and return tickets right here.

Find the cheapest month to fly from Panama City to San Juan

We’re always keeping an eye on fares, so you can find the best one in seconds. It looks like Panama City to San Juan flights are currently cheapest in September.

Direct flights from Panama City to San Juan

Alternative Panama City to San Juan routes

Looking for the cheapest, fastest or easiest route from Panama City to San Juan? You could fly into the following airports instead.

Panama City to San Juan: Flight information

The things to know before you go.
Cheapest flight foundRs51,082
Cheapest month to flySeptember
Average flight time2 hrs, 51 mins
Most popular airlineCopa
Average flights per week84

Finding cheap flights from Panama City to San Juan: Frequently asked questions

There are 6 airports in San Juan: San Juan Isla Grande, San Juan Luis Munoz Marin, Roosevelt Roads, Ponce, Vieques, and Culebra.
The best price we found for a return flight from Panama City to San Juan is Rs85,321. This is an estimate based on information collected from different airlines and travel providers over the last 4 days and is subject to change and availability.
2 hours and 51 minutes is the average flight time from Panama City to San Juan.
Copa and KLM fly direct from Panama City to San Juan.
As of September 2025, there are 24 flights per week flying from Panama City to San Juan.
The cheapest month to fly from Panama City to San Juan is usually October.
If you're flying from Panama City, the cheapest airport near San Juan is San Juan Luis Munoz Marin – which is 11.3 km away from the centre of San Juan. We've found flights into this airport from Rs85,321.
After crunching the numbers on our flight calendar, we found that it is currently cheapest to fly from Panama City to San Juan on Saturday, 11 October 2025.
Yes – the average flight time is 2 hours and 51 minutes.
We show every price from over 1,200 airlines and travel agents, comparing them all so you don’t have to. If you know you want to fly to San Juan but you’re not ready to book, set up a Price Alert. We’ll track prices for you, and let you know when they rise or fall.
We crunched all the numbers in our flight calendar and it looks like the cheapest time to book a flight to San Juan is around 40 days in advance, so don’t leave your flight to the last minute.
In September, the average temperature is usually around 28°C. August is typically the warmest month in San Juan, when it usually averages around 29°C. You can expect the least rain in February. The coldest month is January, with temperatures averaging 23°C. The rainiest month is September.
The cheapest airline that flies to San Juan is Avianca. And the cheapest airline that flies to San Juan Luis Munoz Marin Airport is Copa.

Flying from Panama City to San Juan: what you need to know

  • There are two main airports you can fly out of in Panama City. Check out your options departing from Tocumen International Airport (PTY) or Panama Pacifico Airport (BLB) when searching for a flight from Panama City to San Juan.

  • Luis Munoz Marin International Airport (SJU) is where your flight will arrive in San Juan.

  • Take a direct Panama City to San Juan flight and you'll be travelling for an average of 2 hours 50 minutes.

  • The timezone in San Juan is UTC-4, which is one hour ahead of Panama City.

  • Tocumen International Airport (PTY) to Luis Munoz Marin International Airport (SJU) is the most popular route that connects these two cities. There are 15 flights a week to choose from. If you have things to do before leaving, the last flight from Panama City to San Juan is with Copa Airlines at 18:50. Opt for the first PTY to SJU departure with Copa Airlines at 09:12 to fit in more activities on your first day in San Juan.

  • For a relaxed travel experience, arrive at the airport two hours ahead of international flights and one hour before domestic departures. This leaves you with plenty of time to catch your Panama City to San Juan flight.

  • You can expect bigger queues in popular months like June. Arriving up to four hours in advance for an international flight and two hours for a domestic departure will help ensure a smooth travel experience.

How to find the cheapest flights from Panama City to San Juan

  • To snag cheap Panama City to San Juan flights, book your journey two months ahead of your departure.

  • Organise your trip for May. That's the best month for landing cheap plane tickets from Panama City to San Juan. If you're flexible with your dates, use the 'Whole month' tool to find the cheapest price across each month.

  • Save time searching for cheap flights from Panama City to San Juan by setting up a Price Alert. You'll get an email or push notification on the app when a new discounted fare appears.

  • Tailor your flights using filters. Select your arrival and departure times, total journey duration and airlines. You can also sort your results by 'Best,' 'Fastest' or 'Cheapest' Panama City to San Juan flights.

Flying from Panama City

Tocumen International Airport (PTY)

  • Depart from Tocumen International Airport (PTY) on a nonstop flight from Panama City to San Juan. From PTY, you can travel directly to Luis Munoz Marin International Airport (SJU).

  • Check out the promotions with Copa Airlines. This carrier offers direct Panama City to San Juan plane tickets from PTY.

  • Consider adding a stopover to potentially save on your Panama City to San Juan flight. Simply uncheck 'Direct flights only' when searching for departures from Tocumen International Airport. Break up your trip (and maybe save some cash) by stopping at one of these popular options:

    • Jose Maria Cordova International Airport (MDE)

    • Punta Cana International Airport (PUJ)

    • Las Americas International Airport (SDQ)

  • Travelling from central Panama City to PTY takes around 1 hour 5 minutes by public transport. If you ride-share, drive or get a cab, you'll cover the 18 kilometres in 20 minutes or so, depending on traffic.

  • Planning to catch an early flight from Panama City to San Juan? Avoid rushing to the airport (and enjoy a little extra shut-eye) by choosing one of these stays near Tocumen International Airport:

  • Tocumen International Airport maintains a strong on-time performance, so you're less likely to experience disruptions. Departures from PTY arrive at their destination as scheduled 86.03% of the time.

Panama Pacifico Airport (BLB)

  • Think about adding a stop at El Dorado International Airport (BOG). It's a popular stopover on a Panama City to San Juan flight out of Panama Pacifico Airport. Use a long layover to explore nearby, or take advantage of a short break to get a snack at the airport.

  • Depending on road traffic, you can drive to BLB from the centre of Panama City in around 20 minutes. The airport is roughly 11 kilometres away.

  • Get a head start on your holiday with an additional night away from home. Before catching your flight from Panama City to San Juan, unwind in one of these hotels near Panama Pacifico Airport:

  • Panama Pacifico Airport has a track record for punctuality. 87% of flights leaving here land precisely when expected.

Arriving in San Juan

Luis Munoz Marin International Airport (SJU)

  • Luis Munoz Marin International Airport (SJU) is approximately 11 kilometres from the centre of San Juan. If you're catching a cab or a ride-share, the drive takes roughly 10 minutes.

  • Travelling to the centre by public transport will take you roughly 55 minutes.

  • Consider booking a hotel close to SJU if you're coming in on a late flight from Panama City to San Juan. Select one of these options and avoid the hassle of a long transfer:

  • Hit the road running by picking up a Luis Munoz Marin International Airport rental car. Grab a set of wheels from Sixt, Ace Rent a Car or U-Save and experience the lesser-explored corners of San Juan and beyond.

  • Reserving your vehicle from Luis Munoz Marin International Airport around two weeks ahead gives you the best shot at securing a great deal.

Fernando Luis Ribas Dominicci Airport (SIG)

  • The centre of San Juan is approximately 6 kilometres from Fernando Luis Ribas Dominicci Airport (SIG). After your flight from Panama City to San Juan has hit the runway and you've made your way out of the airport, expect a drive of about 15 minutes.

  • If you travel by public transport, you'll get to the city centre in 1 hour or so.

Best time to go to San Juan

  • It's time to figure out your trip dates for your flight from Panama City to San Juan. July is the most popular month to travel to San Juan. If you prefer a quieter vibe, go in May.

  • The warmest month in San Juan is September, with temperatures ranging between 23ºC and 33ºC. Lock in your Panama City to San Juan ticket then if that's your definition of good weather.

  • For cooler conditions, search for a cheap flight from Panama City to San Juan in February when temperatures average between 20ºC and 28ºC.

More about San Juan

  • When it comes to searching for somewhere to rest your head, you'll find the most popular stays in San Juan right here. Explore these options after you've booked your flight from Panama City to San Juan:

  • There are so many things to discover in this city it can be tricky to know where to begin. Castillo San Felipe del Morro, La Garita del morro de san juan bahia and Fortaleza Street are top sights which should be on any well-planned San Juan itinerary.

Explore more of Puerto Rico

  • You've done San Juan, now it's time to explore more of Puerto Rico. Journey about 10 kilometres west to Bayamon to tick off its leading attractions. From Plazoleta Ignacio Zorrilla, La Plaza de la Bomba Puertorriqueña to Monumento a los Trovadores and Parque Palm Court, there's plenty to keep you on the go.

  • Around 11 kilometres east of San Juan, Carolina is another favourite stop in Puerto Rico. Experience this destination's highlights firsthand at Isla Verde Beach, Parque de Doble A Roberto Clemente Walker and Drone Zone Track.

Prices shown on this page are estimated lowest prices only. Found in the last 45 days.