No injuries were reported.
Television images showed pilings burning in the Harlem River under the 138th Street lift bridge and FDNY marine units hitting the fire with water. Huge orange flames were visible, and plumes of white and black smoke wafted over the river and East Harlem.
The fire began shortly before noon and was declared under control around 1:30 p.m.
Metro-North resumed service around 2:30 p.m., with scattered delays of up to 15 minutes. It said two of the four tracks on the bridge had been restored. The railroad was assessing damage on the remaining tracks and its impact, if any, on the evening rush-hour.
Riders were instructed to use subway connections during the Metro-North shutdown.
The fire department said the cause of the fire was not immediately known.
Suburban commuters have had a tough go of it recently. The Long Island Rail Road suffered a week of service disruptions following an Aug. 23 fire in Jamaica, Queens, that damaged a switching system. On Thursday evening, a storm left downed trees on the tracks, causing LIRR suspensions.