Amtrak says it has finished track repairs following Monday's derailment at Penn Station.
The MTA says Long Island Rail Road service was back to normal for the start of Friday's evening rush.
Amtrak also said its trains are running on schedule again.
Local agencies and officials slammed Amtrak for not making repairs fast enough.
An MTA spokeswoman says the agency is taking a closer look at its relationship with the company.
"We're certainly going to take a look at the operating agreement that we have with Amtrak and what we need to do going forward with that," said MTA spokesperson Beth DeFalco.
Five people were hurt when a New Jersey Transit train derailed Monday morning.
Amtrak's CEO said weakened wooden ties that run under the rails caused the incident.
It was the second train derailment at Penn Station in less than two weeks.