The suitcase was left outside a convenience store near Eighth Avenue and Irving Street at about 7:20 a.m., San Francisco police Lt. Troy Dangerfield said.
The Police Department's bomb squad responded, and police cordoned off the area and shut down service on San Francisco Municipal Railway's N-Judah line, Dangerfield said.
The bomb squad determined that the suitcase was empty and harmless, fire department spokeswoman Mindy Talmadge said.
Police and fire crews were beginning to clear the scene as of about 9 a.m., and Muni service was returning to normal.