|Champions||Wright State(5th title)|
|Winning coach||Greg Lovelady(2nd title)|
|2016 Horizon League baseball standings|
|+ – Conference champion |
? – Tournament champion
y – Invited to the NCAA Tournament
As of June 4, 2016; Rankings from Collegiate Baseball
The 2016 Horizon League Baseball Tournament will be held from May 25-28. The top six finishers of the league's seven teams will meet in the double-elimination tournament to be held at the home field of the regular season champion. The winner of the tournament will earn the conference's automatic bid to the 2016 NCAA Division I Baseball Tournament.
The league's teams will be seeded one through six based on winning percentage, using conference games only. They will then play a double-elimination tournament. The teams seeded three through six will play play-in games. The winners of those games will join seeds one and two to play a double-elimination tournament. The seventh place team will not qualify for the tournament.