Assigned to 'A' Troop under the command of Captain Nicholas M. Nolan, he became the first nonwhite officer to lead buffalo soldiers of the 10th Cavalry.

Flipper served with competency and distinction during the Apache Wars and the Victorio Campaign, but was haunted by rumors alleging improprieties.

After losing his commission in the Army, Flipper worked throughout Mexico and Latin America as an assistant to the Secretary of the Interior.

A review found the conviction and punishment were "unduly harsh and unjust" and ordered Flipper's dismissal be changed to a good conduct discharge.

Eventually, President Bill Clinton posthumously pardoned Lieutenant Henry O. Flipper on February 19, 1999, 118 years after his conviction.

[2][non-primary source needed] In July 1877, Flipper reported to Fort Sill in the Indian Territory, for assignment with the 10th Cavalry.

Finally, Flipper received orders to report to Fort Concho in West Texas in October 1877 and was assigned to 'A' Troop.

Nolan was censured by several white officers for allowing Flipper into his quarters for dinner, where his daughter Kate was present.

[6][7] In August 1878, Captain Nolan married his second wife, Anne Eleanor Dwyer, in San Antonio, Texas.

Anne's sister, Miss Mollie Dwyer, arrived shortly after Troop A moved to Fort Elliott in Texas in early 1879.

[6] In the fall of 1879, a Federal Marshal named Norton, armed with blank warrants, began a quarrel with a county judge.

In the later part of 1880, Flipper was transferred to Fort Davis in West Texas and assigned as the post quartermaster and commissary officer.

[8] Realizing this could be used against him by officers intent on forcing him out of the army, he attempted to hide the discrepancy, which was later discovered, and then lied about it when confronted.

Despite appeals, and with the denial of a lighter sentence from President Chester A. Arthur, Flipper was drummed out of the army with a dismissal, the officer equivalent of a dishonorable discharge, on June 30, 1882.

Flipper spent time in Mexico where, according to folklorist J. Frank Dobie, he attempted to discover the location of the legendary lost silver mine of Tayopa.

[2] He was buried in the family plot at South-View Cemetery, but in February 1978 he was exhumed and reburied in his home town of Thomasville.

On October 21, 1997, a private law firm, Arnold & Porter, filed an application of pardon with the Secretary of the Army on Flipper's behalf.

[citation needed] Many pardon applications had been rejected in the past – as a matter of policy – because the intended recipients were deceased.

Since then, an annual Henry O. Flipper Award has been granted to graduating cadets at the academy who exhibit "leadership, self-discipline, and perseverance in the face of unusual difficulties.

In the posthumous Negro Frontiersman: The Western Memoirs of Henry O. Flipper (1963), he describes his life in Texas and Arizona after his discharge from the Army.