Toucan Travel offers a shuttle service from Puerto Jimenez to San Isidrio, Dominical, Uvita, Palmar, Kilometro 84 (near Ciudad Neily) and San Jose – trips cost between $20-$35 depending on the destination. The shuttle also runs from San Jose to Jimenez.
There is a bus station at the edge of town that goes to destinations such as Rincon, La Palma and Bahia Drake. The schedule is not always posted, and it changes from high to low season, so it's a good idea to verify times before you make any plans. There are also a few pick up and drop off points in town besides the main station, so make sure you know from where your bus will be leaving.
A colectivo makes two trips daily, except on Sundays, to Matapalo and Carate, leaving Jimenez at 6a.m. and 1:30p.m. and costing around $7.
Puerto Jimenez has an air strip, but at the time of writing it was under construction, meant to open in December, 2008. When the strip is operational you can catch Sansa or Nature Air flights to and from other major cities in Costa Rica. Alfa Romeo air taxi also offers flights from Jimenez to Carate, Corcovado Park, Tiskita lodge (in Pavones), Golfito and Drake.
Ferries come and go between Jimenez and Golfito a few times a day, from roughly 6a.m. until 2p.m.; the fare is around $4. There is also a slower boat, the lancha, that makes two round trips daily, leaving Jimenez at 6a.m. and 11:30 a.m. for $2 a person (extra for big luggage). That trip takes an hour and a half. The faster boats take only half an hour.