The mission of the university is "to prepare professionals with broad and deep expertise in their area of study to fill the needs of Tabasco and the country at large."

The origin of the university dates back to 1860, when the governor of Tabasco, Víctor Dueñas, asked President Benito Juárez for funds to establish a secondary, preparatory, and college-level educational institution to serve the community of Tabasco; such funds were granted a year later.

This took place with the support of governor Simón Sarlat Nova and the liberal politician and writer Manuel Sánchez Mármol, who became the first director of the institution.

[7] The first enrollment consisted of less than 100 students in nine academic disciplines: agriculture, veterinary medicine, land surveying, public notary, law, management, education, jurisprudence, and pharmacy.

Adolfo López Mateos, President of Mexico, inaugurated the Zona de la Cultura, or Cultural Zone, at the site where the University currently has its main campus on Avenida Universidad.

[13] "As a result, a significant number of the degree programs offered at the old Institute's location were moved to their new quarters.

"[15] In July 1966, the university started the process of decentralization with the separation of its Preparatory School, and the construction and inauguration of the College of Veterinary Medicine on the Villahermosa-Teapa Road.

There is also an extension program (formally, the Multidisciplinary College of los Ríos) that operates from the town of Tenosique.

With an initial budget of 38 million Mexican pesos, this new location will be called the Multidisciplinary Division of Comalcalco.

September 11, 2008, saw the accreditation of two more academic programs in the College of Agricultural and Fish Sciences: agronomy and food engineering.

In an ATEI Informa newsbrief dated October 12, 2006, the Asociación de Televisión Educativa Iberoamericana (Association of Ibero-American Educational Television) reported that "UJAT was among the 16 best universities in the country when it received an acknowledgement to that effect granted by the Secretary for Public Education.

The university integrates intramural sports, physico-culture, fitness, band, and ballet teams amongst its extracurricular offerings.

One such agreement is with the Texas A&M University "intended to create an environment conductive to the broadening and strengthening of its programs".

[35] The university also houses, via the College of Life Sciences, the Centro de Transferencia Tecnológica Para La Acuacultura (CETRA).

As of February 2009, the university had approved the opening of a Centro de Investigaciones sobre Energia, Agua, y Cambio Climatico, or Research Center for Energy, Water, and Climatic Change.

[37] In April 2009, the university opened the Centro de Integración Ovina del Sureste (CIOS), or The Southeastern Center for Ovine Integration, in the College of Fish and Agricultural Sciences.

[38] Since 1986, the university has moved along in a meaningful manner towards consolidating its areas of research, not only by diversifying its centers, projects, and research programs based on their respective fields of study, but also by striking collective agreements and inter-institutional relations with both academic and non-academic institutions with the purpose of increasing participation and financing.