British Transport Police were called to the line close to Abbey Road in Kirkstall shortly before 6.30pm.
A spokesman said: "Officers attended alongside paramedics, however, a 33-year-old man was pronounced dead at the scene. His family have been told.
"The man’s death is not being treated as suspicious and a file will be prepared for the coroner. "
All lines were closed between Leeds and Shipley while emergency services worked at the scene.
A number of Northern Rail services were suspended or cancelled, with a replacement bus put in place until lines reopened.