One train out of two was expected to run on the Paris suburban RER B line, while the RER A line was expected to be normal, an RATP official said.
Services on the capital's metro line, which had been severely affected on Tuesday, were expected to be "almost normal," the official added.
Other unions are expected to vote on resuming strike action, with the SNCF national rail company saying services will likely be as badly disrupted.
On Tuesday, it ran just one in three trains on Tuesday.
International train traffic was expected to return to normal Wednesday with Eurostar services unaffected by strike action.
Tuesday's nationwide protests were the biggest since the pensions reform battle began earlier this year, unions and police said.
Other sectors hit by continiuing strikes on Wednesday included:
- Oil refineries - half the countries' refineries were reported closed with fears of fuel shortages rising;
- School students refused to attend classes at at least 135 schools after joining protests in large numbers on Tuesday;
- Council workers, with garbage disposal disrupted in the southern city of Marseille;
- Velib' - the Paris city's bicycle service is expected to be disrupted.