After the war, Wilkinson decided to turn to teaching. For a year he taught military science at Howard University, and then was appointed as an aide-de-camp to Major General Oliver Otis Howard––then President of Howard University and the Commissioner of the Freedman’s Bureau. It was during this time when Wilkinson made his first significant contribution to Indian education. While Howard University’s main focus at the time was to educate freed slaves, Wilkinson argued that there should also be an opportunity for Indians to attend the college. In 1872, Wilkinson spent a year with General Howard in the Southwest, helping to resolve problems with the Apache tribe. Between 1871 and 1875, Howard successfully enrolled several Indian children. This was an early milestone for the creation of off-reservation boarding schools, which Wilkinson would later be a part of.
