The 1999 Hofstra Flying Dutchmen football team represented Hofstra University during the 1999 NCAA Division I-AA football season. It was the program's 59th season, and they competed as an Independent. The Flying Dutchmen earned a berth into the 16-team Division I-AA playoffs as the #3 seed, but lost in the quarterfinals to Illinois State, 37–20. They finished #5 in the final national poll and were led by 10th-year head coach Joe Gardi.