The 1989 NCAA Division III Men's Ice Hockey Tournament was the culmination of the 1988–89 season, the 6th such tournament in NCAA history. It concluded with Wisconsin-Stevens Point defeating RIT in the championship series with 1 win and 1 tie. All Quarterfinals matchups were held at home team venues, while all succeeding games were played in Rochester, New York.

The following teams qualified for the tournament. There were no automatic bids, however, conference tournament champions were given preferential consideration. No formal seeding was used while quarter and semifinal matches were arranged so that the road teams would have the shortest possible travel distances. Because the semifinal series were played at home team venues the NCAA elected to select an equal amount of eastern and western teams.

The tournament featured three rounds of play. Starting in 1988, each round of the tournament consisted of a two-game series where the first team to reach 3 points was declared a winner (2 points for winning a game, 1 point each for tying). If both teams ended up with 2 points after the first two games a 20-minute mini-game used to determine a winner. Mini-game scores are in italics. The teams were seeded according to geographic proximity in the quarterfinals so the visiting team would have the shortest feasible distance to travel.

Note: * denotes overtime period(s)
Note: Mini-games in italics