If you only have three days in Panama, I wouldn't try to cram in Bocas del Toro, Boquete or San Blas. You'll spend too much of your trip traveling.
Instead, I'd build the trip around Panama City + the Canal + Portobelo + El Valle de Antón. That gives you an incredible mix of city, history, Caribbean culture, jungle, mountains and adventure without spending your entire vacation on buses.
🇵🇦 DAY 1 — Panama City: Canal, Casco & the Skyline
Morning — Panama Canal
Start early at the Miraflores Locks.
Give yourself around 1½ to 2 hours to watch ships move through the locks and visit the exhibits. The canal is one of those attractions where photographs really don't convey the scale until you're standing there watching a gigantic container ship being lifted several meters by water.
Afterward, head back toward the center of Panama City.
Late Morning — Casco Antiguo
Spend the late morning wandering around Casco Antiguo.
Don't rush it. Walk through the plazas, explore the old churches, look at the colonial buildings and wander along the waterfront. The historic district was established in 1673 after the original Panama City was destroyed, and its ruins and architecture tell an enormous part of Panama's story.
Have lunch somewhere around Casco.
Afternoon — Cinta Costera & Amador
After lunch, walk or take a taxi toward the waterfront and spend some time along the Cinta Costera.
Then head out toward the Amador Causeway. This is a great place to see Panama City from the opposite perspective, with the Pacific in front of you and the skyscrapers behind you.
If you're interested in museums, this is also where you can visit the Biomuseo.
Evening — Casco Antiguo
Come back to Casco for sunset.
This is when I'd slow down. Find a rooftop, have a drink or dinner and watch Panama City's skyline light up.
Sleep: Panama City, preferably around Casco or somewhere with easy access to the old town.
🏴☠️ DAY 2 — Portobelo: Pirates, Forts & the Caribbean
This is the day that turns the trip from a standard city vacation into a Panama adventure.
7:00–8:00 AM — Leave Panama City
Head toward the Caribbean side of the isthmus.
Portobelo is fascinating because it isn't simply a pretty Caribbean town. It was once one of the Spanish Empire's most important ports, where enormous quantities of treasure passed through on their way to Europe.
That history also made it a target for pirates.
Morning — Explore Portobelo
Spend a few hours walking around the historic town and exploring the old fortifications.
Visit Fort San Jerónimo, the remains of the other colonial defenses and San Felipe Church, famous for the Black Christ. The official tourism authority highlights the forts, church, old customs house and Afro-Panamanian history as some of Portobelo's major attractions.
This is also where you can really get into the pirate history of Panama.
Portobelo isn't polished like a major resort. That's part of its charm.
Lunch — Caribbean Food
Have lunch in Portobelo or nearby.
Look for seafood and Afro-Caribbean dishes. Coconut, seafood and local spices are a big part of the culinary character of the Caribbean coast.
Afternoon — Add a Beach or Boat Trip
If you have a car or arrange a boat, spend the afternoon exploring the coastline.
The Portobelo district contains numerous beaches and islands, and boats can take visitors toward places such as Playa Blanca, Playa Puerto Francés and Isla Grande.
If you only have one day, I would not try to see everything.
I'd choose:
Portobelo forts + town and Caribbean lunch and one beach/boat excursion and return to Panama City.
Evening
Return to Panama City.
Have dinner somewhere around Casco or El Cangrejo and get some sleep.
Sleep: Panama City.
🌋 DAY 3 — El Valle de Antón
This is the day I'd leave the skyscrapers completely behind.
El Valle de Antón sits inside the crater of an extinct volcano and is roughly 2½ hours from Panama City, making it possible as a long day trip.
6:30–7:00 AM — Leave Panama City
The earlier you leave, the better.
You want as much time as possible in the mountains.
Morning — La India Dormida
Start with a hike.
La India Dormida is probably the iconic choice for a first visit. The trails climb into the mountains surrounding the valley and provide fantastic views over the crater.
If you're a serious hiker, there are other routes around the caldera, including La Silla, Cara Iguana and El Gaital. The official tourism authority describes the Caldera Route as a network of trails ranging from easier walks to challenging climbs.
Lunch — El Valle Market
Come back into town and have lunch around the central market.
This gives you a chance to see another side of Panama: fresh fruit, local food, handicrafts and the slower pace of a mountain town.
The craft market is also a good place to pick up something genuinely Panamanian rather than another generic souvenir.
Afternoon — Waterfall or Hot Springs
Now choose your adventure.
Option A: Chorro Las Mozas
Easy walks lead to waterfalls and natural swimming pools surrounded by vegetation.
Option B: Chorro Macho
Go for the waterfall and, if you're feeling adventurous, the canopy/zipline experience through the forest.
Option C: Hot springs
If you're exhausted from the hike, head for El Valle's thermal pools instead. The town's hot springs are a classic local activity.
Late Afternoon — Head Back to Panama City
Leave El Valle with enough time to get back before the evening gets too late.
Have your final dinner in Panama City.
🗺️ Your 3-Day Route at a Glance
Day Morning Afternoon Evening
Day 1 Panama Canal Casco + Amador Casco nightlife
Day 2 Portobelo forts Caribbean beach/boat trip Panama City
Day 3 El Valle hike Waterfall/hot springs Return to Panama City
🚐 How I'd Do It
For this particular itinerary, a rental car or private driver makes a huge difference.
The biggest advantage isn't luxury. It's time.
With only three days, you don't want to spend hours waiting for connections. Portobelo and El Valle are both very doable, but the schedule becomes much easier when you can leave when you want and stop along the way.
El Valle can also be done independently by bus from Albrook, but a day trip is considerably easier if you have your own transportation.
If you're a backpacker on a budget
I'd simplify it slightly:
Day 1: Canal + Casco + Cinta Costera
Day 2: Portobelo by bus/shared transport
Day 3: El Valle by bus
And I'd skip trying to add San Blas. It's spectacular, but squeezing it into this itinerary would make the trip feel like a transportation marathon.
⭐ Why I Like This Itinerary
In just three days, you experience four completely different Panamas:
Panama City and modern skyscrapers, nightlife and the Canal.
Casco Antiguo and Spanish colonial history and pirate-era Panama.
Portobelo and Caribbean culture, forts, jungle and the country's extraordinary Afro-Caribbean heritage.
El Valle and volcanic mountains, waterfalls, rainforest and cool highland air.
That's a much better introduction to Panama than spending all three days inside the capital.
And if you have one extra night, I'd make El Valle an overnight rather than a day trip. That turns Day 3 from a rushed excursion into a much more relaxed mountain experience.