As colonel of the 5th Cavalry, Merritt was a member of the court of inquiry which first sat on January 13, 1879 presided over by Colonel John H. King of the 9th Infantry, which was convened to consider the behavior of Major Marcus A. Reno of the 7th Cavalry at the Battle of the Little Bighorn (June 25 to 26, 1876); which resulted in the death of General George Armstrong Custer and over 200 men of the 7th Cavalry.