Out of all the popular cities in Puerto Rico, San Juan is the cheapest city to rent a car in at just $26/day. Renting a car in San Juan is 76% cheaper than renting one in Culebra where the per day rate is around $106. Other fairly inexpensive cities in Puerto Rico to get a rental car in are: Mayagüez ($27/day), Aguadilla ($29/day), and Ponce ($33/day). While these cities typically have cheaper prices than the rest of the country, travelers looking to rent a car in San Juan should expect to spend around $26/day on their transportation. The most popular city to rent a car in Puerto Rico is San Juan.