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The quickest option is a 20 minute flight from the San Jose airport domestic terminal (right beside the international terminal) to Quepos/Manuel Antonio airport. You fly in smaller planes with stunning views. There are flights only during daylight hours as smaller airports in CR don't have night time runway lights. Skyway Airlines twin engine planes fly into Quepos/Manuel Antonio 4 times a day from San Jose and can also take you to all major destinations around Costa Rica. The cost 1 way is as low as $68US. Our link below takes you to their booking site.
Costa Rica has many shared and private van shuttle services from. Travel in modern vans with A/C, and professional drivers. PIck ups occur from various hotels in San Jose and in Manuel Antonio. The trip takes about 3 hours on an excellent and picturesque highway. The cost is around $60US each way. Also available to get to Manuel Antonio from all major destinations in Costa Rica.
Another option is to rent a taxi from the stand in the airport - or ask your hotel to send a taxi to the airport. The normal cost is $125 to $150US and it takes about 3 hours on an excellent highway.
Safe reliable comfortable public buses run every hour from Tracopa Station in central San Jose to Quepos/Manuel Antonio for about $10US. The trip takes about 4 hours. This is a good option if your staying in central San Jose before coming to Manuel Antonio.
The drive from San Jose to Quepos is 170 km and takes 2 1/2 to 3 hours, depending on the traffic. Expect a slow drive, the maximum speed limit in Costa RIca is 80km/hr. There are a wide variety of rental car companies. Basic personal liability insurance is required to be purchased at the rental car company in Costa Rica, and is usually not included in the quote you may have received. Car damage insurance may be purchased seperately, but your credit card, if used to pay for the car rental, likely will cover this. Check with your credit card and bring a copy of the policy - saving you from buying this additional insurance at a significant cost.