The central building had previously belonged to the Seminario Conciliar (Council Seminary), a Jesuit institution that specialized in training priests and lawyers.

The foundation of the Civil College was part of a struggle between church and state that played out in Mexican higher education in the second half of the 19th century.

When it started, the Civil College began to lure academics, resources and endowed chairs from the Seminario, which ultimately closed in 1859.

In 1938, with the incorporation of Instituto Juárez into the University of Mexico, the school took on the motto of that institution ("Por mi Raza hablará mi espíritu", or The Spirit shall speak for my race), its colors of blue and gold, and its current seal.

This decision was made in an attempt to lure and keep faculty, develop a more educated populace in the state, and increase the number of professionals in Durango.