San Juan College was founded in 1956 as the Farmington Branch of the New Mexico College of Agriculture and Mechanical Arts, in accordance with statutes of the State of New Mexico. In 1958, the name was changed from Farmington Branch to San Juan Branch, NMSU. This name better indicated the area served by the branch. The school became San Juan College in 1982.
San Juan College offers associate's degrees and certificates from the following schools:
- School of Business
- School of Energy
- School of Health Sciences
- School of Humanities
- School of Science, Math and Engineering
- School of Trades and Technology
Several degrees and certificates are available in fully online formats through the distance learning program.