In 1882, he returned to Cornell University, completed his studies and graduated. In 1883 to 1885, he was topographic geologist of the Geological Survey of Pennsylvania in the anthracite regions; in 1885, after receiving his Ph.D. from Indiana University, he was made professor of geology at Indiana University, a position he held until 1891, though he was absent on leave for several years. In 1887, he was appointed State Geologist of the Geological Survey of Arkansas. As State Geologist, he exposed gold-mining swindles then operating in Arkansas, for which the citizens of Bear City, Arkansas, burned him in effigy, and the stock promoters tried to have him fired. In 1891, he was appointed Professor and Chair of the Department of Geology at the newly opened Stanford University, recruited by his colleague from Cornell and Indiana, Stanford President David Starr Jordan. When Jordan retired as president of Stanford in 1913, Branner was elected President of the university. He retired January 1, 1916, due to an age limit established by the university and was named President Emeritus.