After the war, Walker was recommended for the Medal of Honor by Generals William Tecumseh Sherman and George Henry Thomas. On November 11, 1865, President Andrew Johnson signed a bill to present her the medal, specifically for her services at the First Battle of Bull Run (Manassas).

In 1917, the U.S. Congress, after revising the standards for award of the medal so that it could only be given to those who had been involved in "actual combat with an enemy", revoked more than 900 previously-awarded medals, including that of Dr. Mary Edwards Walker and William F. "Buffalo Bill" Cody. Although ordered to return the medal, she refused to do so and continued to wear it until her death.

President Jimmy Carter restored her medal posthumously in 1977.