Waggener was born in Trenton, Kentucky, and earned degrees from Bethel College in 1860 and Harvard University in 1861. During the American Civil War, he fought in the Confederate Army. He then became a professor of English at Bethel and became chairman of the faculty in 1873. Sometime between 1875 and 1877, he became the college's president, a position he held until 1883. He earned a master's degree from Bethel in 1867 and a doctorate from Georgetown College in 1875.[2][3][4]
He joined the University of Texas in 1883 as an English literature and history professor in its inaugural faculty. From 1884 to 1894, he was elected as chairman of the faculty. Waggener became the university's first president in 1895 upon the creation of the office, serving in an interim role for one year. He also was the president of the Texas State Teachers Association for one year.[3][4][5][6]