The train, which derailed early Sunday morning, is known in Mexico as La Bestia, or the Beast, The Wall Street Journal reported.
Central American migrants frequently jump aboard the train for a free, dangerous ride in their attempted reach the United States.
Luis Felipe Puente, the coordinator of emergency services at Mexico's Interior Ministry, said 35 people were injured in the accident.
Sixteen were injured seriously, Puente said.
Rescue teams faced difficulties in reaching the site, and the cause of the accident wasn't immediately known, the Journal reported.