This seminary had its origins in the Austin School of Theology, begun in 1884 by the Rev. Dr. Richmond Kelley Smoot and the Rev. Dr. Robert Lewis Dabney to provide training for candidates for the Presbyterian ministry whom the founders hoped would remain in Texas and the southwest. Smoot and Dabney both taught classes, but received no compensation. Although the school closed in 1895, continuing enthusiasm for a permanent seminary provided momentum to the Synod of Texas to appoint a committee to carry out this vision.
The new institution opened in 1902 as the Austin Presbyterian Theological Seminary, with the Rev. Dr. Thornton Rogers Sampson as President. Classes were held at an east Austin campus in a donated building. Wishing to take advantage of an academic partnership with the University of Texas, Sampson succeeded in moving the seminary campus to this site in 1908. Smoot's and Dabney's original goal of having seminary students remain in the region was realized, as graduates accepted calls to pastorates in Texas, Arkansas, Oklahoma and Louisiana.
After World War I, Austin Presbyterian Theological Seminary began a Spanish-speaking department to serve the Hispanic population in south Texas. Other programs have developed over the years to equip Presbyterian pastors with training and education for ministry in a rapidly changing world.