The railroad says all trains are running with scattered delays of up to 15 minutes until 10 p.m. After 10 p.m., bus service will connect commuters to shuttle train service.
A freight train hauling garbage derailed between stations Thursday night.
The derailment affected service on the line that runs between Manhattan and Poughkeepsie, 80 miles north.
The damage was so substantial that only one of two tracks in the area is back in service on Monday. Work will continue on rebuilding the other track before it can be returned to passenger service.
The cause of the derailment is under investigation by the National Transportation Safety Board.
New York senator Charles Schumer is asking investigators to look at whether the recent heat wave weakened the railroad's fragile infrastructure.
"Some of the equipment along these lines dates back to 1914," says Schumer, "It's 100 years old. It means this equipment is particularly susceptible to transit-related failures."
Metro North's Hudson Line ferries thousands of people from Dutchess, Putnam, Westchester and the Bronx into Manhattan, and the derailment is causing major headaches for commuters.