The town was founded in 1801 by Antonio Gonzales and was named in honor of Saint Thomas. During the colonial era the land was used primarily for ranching. Pure quality cannel coal was found and extracted in 1873.
By 1900, the town grew and had a population of approximately 1,000. By 1920, all the mines closed and the population of Santo Tomás decreased to 18. Today, Santo Tomás is a ghost town near the Colombia-Solidarity International Bridge.