Flipper was born into slavery in Thomasville, Georgia, on March 21, 1856 and was educated once the Emancipation Proclamation freed him and his parents.
In 1873 he received an appointment to attend West Point. He was not the first black student: there were four other black cadets already attending when he came.
The small group had a difficult time at the academy, where they were rejected by white students. In his 1878 autobiography, The Colored Cadet at West Point, Flipper describes how white professors and cadets refused to speak with him. Faced with social ostracism, he had to be content with "a pleasant chat every day, more or less, with the bugler, the tailor, the barber, and other workers at the school.
In spite of the isolation, Flipper persevered. In 1877, he became the first African American to graduation from West Point and earned a commission as a second lieutenant in the U.S. Army cavalry. He was assigned to Company A of the 10th Cavalry Regiment, which was one of four all-black "buffalo soldier" regiments. He arrived at Ft. Davis, Texas in 1880, where he was the quartermaster and commissary officer.
Until now, all-black regiments had been commanded by white officers. Flipper was the first black officer to command regular troops in the U.S. Army. It appeared that all of Flipper's perseverance was paying off. He seemed to be doing well, and was even praised for his performance during the Victorio War, a short skirmish with the Chihennes Apaches that ranged through southern New Mexico and Texas and spilled over into Mexico.
But Flipper's rise took an unexpected downturn in August of 1881, when he was arrested on suspicion of embezzling funds. Flipper had discovered a shortage of $1,440 in the accounts and instead of reporting it, lied about it. Flipper later testified that he believed the deficit was because of a mistake on his part, and he had determined to make it up over time out of his own monies. His court martial decided that inexperience and carelessness led to the deficiency and, even though the judge advocate general of the army determined that Flipper had not intended to defraud the government, he received a dishonorable discharge from the army in 1882.
In 1976, thirty-six years after his death, Flipper's heirs, requested that his case be reviewed. The Army then issued a certificate of honorable discharge in light of the fact that white officers found guilty of similar charges remained in service, while Flipper did not. It appears Henry O. Flipper was the victim of 19th Century racial prejudice.