The 2013 Florida Atlantic Owls baseball team represented Florida Atlantic University in the sport of baseball for the 2013 college baseball season.

The Owls competed in Division I of the National Collegiate Athletic Association (NCAA) and the Sun Belt Conference.

They played their home games at FAU Baseball Stadium, on the university's Boca Raton, Florida campus.

The team was coached by John McCormack, who was in his fifth season at Florida Atlantic.

FAU players selected in the 2013 MLB First-Year Player Draft: