Flipper was born to enslaved parents but came of age in Atlanta during Reconstruction. He was educated at American Missionary Association schools and Atlanta University (now Clark Atlanta University). In 1873, he was appointed to West Point. As he later wrote in his 1878 autobiography, The Colored Cadet at West Point, he was socially ostracized by white peers and professors during his four years there.
After graduation, Flipper was appointed to serve as second lieutenant in the all-African American 10th Cavalry and stationed at Fort Sill in Oklahoma. The Ninth and 10th Cavalry were regiments of Black enlisted men who became known as the Buffalo Soldiers.
While at Fort Sill, Flipper negotiated with local Native American tribes and supervised several engineering projects, including the building of roads and telegraph lines. A drainage system he designed became known as "Flipper's Ditch" and is listed as a National Historic Landmark.
In 1881, he was accused of stealing over $3,000 in commissary funds and relieved of duty. Though a court-martial found him not guilty of embezzlement, he was dishonorably discharged for "unbecoming conduct" in 1882.
Flipper went on to a distinguished career as a civilian engineer and surveyor, and later served in Washington, D.C. as a consultant on Mexican relations. Flipper maintained his innocence throughout his later years and fought to clear his name. He died on May 3, 1940, in Atlanta, Georgia.
In 1976, the Army upgraded his discharge to honorable. And in 1999, President Bill Clinton granted Flipper a posthumous pardon, saying, "Henry Flipper did all his country asked him to do."