Out of all the popular cities in Puerto Rico, Mayagüez is the cheapest city to rent a car in at just $23/day. Renting a car in Mayagüez is 79% 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: San Juan ($25/day), Aguadilla ($28/day), and Vieques ($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 $25/day on their transportation. The most popular city to rent a car in Puerto Rico is San Juan.