The strike has also affected another rail company Adif, the Administrator of Railway Infrastructures, a state-owned company that plays a leading role in the country's rail network.
The General Confederation of Labour trade union organized the strike to demand the return of bonuses, an end to wage freezes and the hiring of new workers by both Renfe and Adif. The trade union also demanded the unification of rail transport into a single company.
Some 51 out of 306 freight trains will remain in service, 17 percent of normal.
Between 62.5 percent and 75 percent of Spanish commuter trains will provide limited service.
The strike is scheduled to end Friday at 11 p.m. local time (22:00 GMT).
Spain has been in a serious economic, social and political crisis for the past several years. The country has seen many strikes in almost every sector of its economy, largely supported by trade unions.