The 2016 Navy Midshipmen football team represented the United States Naval Academy in the 2016 NCAA Division I FBS football season. The Midshipmen were led by ninth-year head coach Ken Niumatalolo and played their home games at Navy–Marine Corps Memorial Stadium. The Midshipmen competed as a member of the West Division of the American Athletic Conference, and were second year members of the conference. They finished the season 9–5 overall and 7–1 in American Athletic play to be champions of the West Division. They represented the West Division in The American Athletic Championship Game where they lost to Temple. They were invited to the Armed Forces Bowl where they lost to Louisiana Tech.