The Navajo Language Program was founded in 1970 by Dr. Bernard Spolksy under the name of the Navajo Reading Study, as a project of the interdepartmental Program in Linguistics and Language Pedagogy. Its goal was to produce Navajo language materials and promote literacy in the Navajo language. That same year, the Program in Linguistics and Language Pedagogy helped design Navajo language courses, which were taught by Irene Silentman in the Department of Modern and Classical Languages. In 1973, the Navajo Reading Study developed the Teacher Training Project, whose aim was to prepare Navajo educators in bilingual education. While the Department of Modern and Classical Languages continued to offer courses in Navajo, the Navajo Reading Study ended in 1977 with the completion of Dr. Robert Young and Dr. William Morgan’s seminal work, The Navajo Language: A Grammar and Colloquial Dictionary.

Although the Department of Linguistics expressed its desire for the program to continue incorporating research in linguistics and educational linguistics, the program remained in the Department of Modern and Classical Languages for the next ten years. The Navajo Language Program was finally integrated into the Department of Linguistics in 1988. Thanks to the efforts of Roseann Willink, who began as a Navajo instructor in 1980, the program began to offer Navajo language as an undergraduate minor in 2003. Four years later, Dr. Sherman Wilcox, and Dr. Melvatha Chee, who was a graduate student at the time, lobbied with the New Mexico legislature to secure more funding for a tenure track professor, staff, and teaching assistants. In Fall 2019, Dr. Melvatha Chee joined the faculty of the Department of Linguistics and began as director of the Navajo Language Program. Amelia Black was hired as the primary instructor in 2021, and thanks to her expertise the program started using an immersion method of instruction for its introductory courses. The program also started offering online immersion courses in 2021, which has been popular with students who do not live in Albuquerque.

The Navajo Language Program celebrated its 50th anniversary in 2020.