All trains were stopped along the French Riviera after storms and flooding killed at least 16 people, although the pilgrims' trains were allowed to resume their journey at a slow pace on Sunday.
"We hope to let them continue their journey towards Italy by letting their trains go along a track re-opened for them, but at a slow speed," said a spokesman for French rail company SNCF.
The storm "did serious damage to the railway infrastructure, tracks, crossings, electrical lines, primarily around the area of Cannes," he told AFP.
There were conflicting reports from French and Italian authorities over the number of pilgrims affected, with either four or five trains carrying between 1,200 or 2,500 people.
Lourdes, a city in the foothills of the Pyrenees, is a hugely popular site of Catholic pilgrimage.
Some of the pilgrims were elderly or disabled, travelling in carriages with special medical facilities and doctors, although no emergencies were reported.
Six other trains were also trapped overnight by the floods. Their passengers were evacuated once the roads were re-opened, the spokesman said.
All trains were cancelled between Toulon and Nice on Sunday, a route that is widely used to service the French Riviera, and by high-speed trains between France and Italy.