One of the men tumbled into Berry's Creek near the Route 3 bridge and the other went in after him, responders said.
Both were taken to Hackensack University Medical Center with injuries that weren't considered life-threatening, they said.
It was unclear what the men, ages 38 and 40, were doing on the tracks when they were struck by the Bergen Line train from Spring Valley to Hoboken around 12:20 p.m. , NJ Transit's Lisa Torbic said.
Both received summonses for trespassing and interfering with transportation by NJ Transit police, who were investigating, Torbic said.
None of the 10 passengers or crew members aboard the 2110 were injured, she said.
Bergen Line and Pascack Valley Line service was temporarily suspended between Rutherford and Secaucus.
Click here to follow Daily Voice Elizabeth and receive free news updates.