Bus service is also being provided for the Wassaic branch.
Train service also resumed Monday between Port Jervis and Harriman stations on the Port Jervis Line.
Customers should expect residual delays on the Upper Harlem and Port Jervis lines.
Metro-North crews have been working around the clock to clear dozens of downed trees that blocked tracks north of North White Plains.
The freak October nor'easter knocked out power to more than 3 million homes and businesses across the Northeast.
Riders returned to northern Westchester after being stuck on a train for hours Sunday.
"I guess the train lost power for two and a half hours," rider Jessica Mola said.
"I mean three, four hours, I had to cancel my afternoon. Some people were missing shows, some people were missing games, other people were dealing with cranky kids, and the odd panic attack. I think someone almost fainted from the heat," rider Jonathan Estabrooks said.
"I mean there was no oxygen in the car the air conditioning systems and heating systems were all shut off," he added.
The railroad's Upper Harlem line was shut down due to fallen trees north of North White Plains, along with the Wassaic and Danbury branches.
They were problems Governor Andrew Cuomo believes will have minimal impact on the Monday morning commute.
"I'm sure there will be some hangover. We're doing the best we can today but we will be functional and operational tomorrow by and large," Cuomo said.
MTA METRO NORTH: CLICK HERE FOR SERVICE STATUS