The bridge's four tracks carry Metro-North trains in and out of Manhattan.
Metro-North service was suspended at 11:45 a.m. in and out of Grand Central Terminal.
All Metro-North train traffic passes over the bridge on the Harlem River. Like many of the Harlem River bridges, it rarely opens except for periodic testing by the DOT.
The fire burned through wooden piers in the river, which are intended to keep boats from hitting the station.
Marine units hit the fire with water, but huge orange flames were visible and plumes of white and black smoke billowed over the river and East Harlem for nearly two hours.
At Grand Central Terminal, Metro North riders rode out the service suspension in stride.
"You stand around, be in a good mood and hopefully the trains will come back on soon," one woman said.
Unfortunately, not all commuters had the luxury of time and patience.
More than a few struggled to find an alternative to get where they needed to go in the absence of Metro North trains.
"I gotta go up to Fordham road in the Bronx, so I'm trying to figure out what subway to take," Robert Kwit said.
Others use to dealing with the precarious nature of New York City transit came equipped with a back-up plan.
"I'm going to take an alternative. I'm going to take the #4 uptown to Fordham and then take a taxi and go to reach to my job site," Pamela Mitchell said.
The fire was declared under control around 1:30 p.m.
Regular off-peak train service resumed in and out of Grand Central Terminal shortly after 2:30 p.m. with scattered delays of up to 15 minutes.
Two of four tracks on the 138th Street Bridge were restored initially. All four tracks were back up and running by the evening commute.
The railroad carries about 135,000 people into Manhattan each morning.
The NYC Office of Emergency Management reports that the cause of the fire was a transformer.