Following his graduation, Flipper received his commission as second lieutenant, and became the first black officer in the U.S. Army. In 1878, he was assigned to the Black 10th Cavalry Regiment. In November 1881, in an apparent racial incident, he was accused by his white commanding officer of embezzling funds. Although he was acquitted of the charges, he was dishonorably discharged in 1882.
Flipper tried unsuccessfully to vindicate himself for many years thereafter. He died on May 3, 1940, in Atlanta, Georgia. Thirty-six years after his death, in 1976, it was revealed that officers had framed him. President Bill Clinton posthumously granted Flipper an honorable discharge in 1999, and on the 100th anniversary of his graduation, West Point unveiled a bust to honor the former graduate.