A spokesperson said a suspicious package on board train 662 prompted the evacuation. A police bomb squad was called to the scene to inspect the package.
The train was moved from the station as a precaution.
After a delay of over three hours the train was cleared and continued into Chicago without incident.
"The package, the origin of it is under investigation, but it turned out, it was not any sort of device to be concerned about. It turned out to be a container inside a piece of luggage," said Mark Krause of the Harvard Police Department.
Harvard police say they're taking extra precautions due to the upcoming NATO summit.