The 2016 Jacksonville Dolphins football team represented Jacksonville University in the 2016 NCAA Division I FCS football season.

They were led by first-year head coach Ian Shields and played their home games at D. B. Milne Field.

They were members of the Pioneer Football League (PFL).

[1] They finished the season 5–5, 4–3 in PFL play to finish in fifth place.

The game between Jacksonville and Campbell was cancelled in advance of the arrival of Hurricane Matthew.