Out of all the popular cities in Puerto Rico, San Juan is the cheapest city to rent a car in at just $7/day. Renting a car in San Juan is 86% cheaper than renting one in Culebra where the per day rate is around $47. Other fairly inexpensive cities in Puerto Rico to get a rental car in are: Ceiba ($15/day), Mayagüez ($17/day), and Aguadilla ($19/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 $7/day on their transportation. The most popular city to rent a car in Puerto Rico is San Juan.