A vagrant wandering through the F train tunnel between Manhattan and Brooklyn snarled the rush hour commute as cops tried to hunt him down, sources said.

A train operator was driving an F train through the Rutgers Tube at about 4:20 p.m. on Tuesday when a man suddenly jumped onto the tracks. The operator slammed on the brakes and avoided hitting the guy, who then ran off.

F trains ran on the A line between Jay Street-MetroTech and West 4th Street in both directions as police units canvassed for the intruder.

They finally found him at about 5:30 p.m. He was covered with cuts and bruises, but it did not appear that any train struck him, cop sources said. Emergency personnel took him to Woodhull Hospital for evaluation.