The 2016 South Dakota State Jackrabbits football team represented South Dakota State University as a member of the Missouri Valley Football Conference (MVFC) during the 2016 NCAA Division I FCS football season.

Led by 20th-year head coach John Stiegelmeier, the Jackrabbits compiled an overall record of 9–4 with a mark of 7–1 in conference play, sharing the MVFC with North Dakota State.

Due to their head-to-head victory over North Dakota State during the regular season, South Dakota State received the MVFC's automatic bid to the NCAA Division I Football Championship playoffs, where, after a first-round bye, the Jackrabbits defeated Villanova in the second round, before losing in the quarterfinals in a re-match with North Dakota State.

The team played home games on campus at the newly-opened Dana J. Dykhouse Stadium in Brookings, South Dakota.

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