Nacogdoches is home to Stephen F. Austin State University. Since 1923, SFA has been producing graduates with a diverse selection of skill-sets. SFASU offers more than 120 areas of study.

The Arthur Temple College of Forestry and Agriculture is nationally recognized, and houses one of only two schools of forestry in the State of Texas (and the only forestry college in the timber-producing East Texas region). The Forestry program is #2 in Texas.

In addition to the main campus which is located on 430 acres, the university maintains a 642-acre (2.60 km2) agricultural research center for beef, poultry, and swine production and an equine center; an observatory for astronomy research, a 1,072-hectare (approximately 2,649-acre) experimental forest in southwestern Nacogdoches County and a 25.3-acre (102,000 m2) forestry field station on the Sam Rayburn Resevoir.

It is also the home of the National Center for Pharmaceutical Crops, which in 2011 discovered a potential cancer-fighting agent from the extract of giant salvinia, one of the world's most notorious invasive species.