Crews worked through the morning to remove the tree that fell at about 4 a.m. According to a Metro spokesperson, the tree fell on overhead power lines, blocking tracks in both directions.
There were only seven passengers on the commuter train at the time. No one was injured, and those passengers were picked up by a bus.
Gold Line commuters traveling from Pasadena and other northeastern suburbs to downtown Los Angeles had to take a shuttle bus between two stations until service was fully restored at around 1 p.m.
The Associated Press contributed to this report.