Driving a car is inadvisable in San Jose. Not only are the roadways confusing (made just that much more difficult by the city's lack of street names and signs demarcating which streets are one-way), but San Jose drivers are also extremely aggressive, making driving on the roadways a bit like taking your life into your own hands. While on a grid system, many of San Jose's streets are unnamed, and navigating without the use of landmarks such as a church or other building, can be near-impossible. Rather than drive yourself, it is a much better idea to take a taxi, especially since they are so readily available and are relatively inexpensive. Licensed taxis are discernible by their red color and the placement of a gold triangle on the front doors. Even taxi drivers may be confused by an address, so have an idea of what is located nearby your destination to help your driver find his way. Distances in the cities are often marked in metres; 100 metres is considered to be about one city block in length.

The above does not mention one danger about driving in San Jose which is the missing man hole covers and drain covers on so many of the streets.   Shocked after arriving in Costa Rica to see this hidden danger and can't express enough about this problem in Costa Rica and especially in the San Jose area.  Most of the taxi drivers are good; however had several who seemed to joy ride at the expense of the meter.  Taxies are not really that cheap compared to other countries, so, if you don't know where you’re going chances are they won't know either.

Bus service in San Jose is quite reliable and can be taken to locales both within the city and to neighborhoods in the surrounding area. A typical bus fare is 100 colones, although a ride on a luxury bus to the outskirts of the city can cost up to 150 colones.

San Jose is the main jumping off point to reach the rest of Costa Rica. Transportation options range from public buses that make multiple stops in route to 'directos' or buses that take passengers to one main destination (usually the beach or other popular towns or attractions), public shuttles that are reserved in advance, private vans and domestic flights. Prices range greatly from $6 on a public bus for a 5 hour trip to Liberia to $250 for a private van to Manuel Antonio.

Costa Rica's two major airlines, Nature Air and Sansa Regional, offer flights to more than 16 destinations in the country, and Nature Air offers flights between San Jose and Bocas del Toro, Panama as well. A range of private charter companies are also available and include Aerobell, Paradise Air and Nature Air.