The attack was carried out by the Revolutionary Armed Forces of Colombia (FARC), Colombia's largest leftist rebel force, which often strikes at mining operations in northern Colombia.
The bombing caused the derailment of 20 wagons as the train headed away from the nearby Caribbean port of Bolivar in the direction of the mine.
No one was hurt, but transport of 70,000 tonnes a day from Cerrejon to Bolivar will not resume for about five days while repairs are carried out, the mine said in a news release.
FARC are active in the area around the mine, which is located in the Caribbean region of La Guajira. Although Cerrejon has seldom reported attacks, the FARC has often bombed a railway operated by American-owned coal company Drummond in the nearby province of Cesar.
Cerrejon is controlled by a consortium that includes BHP Billiton, Anglo American and Glencore International.
