The 1969 NCAA College Division baseball tournament decided the champion of baseball at the NCAA College Division level for the 1969 season. This was the second such tournament for the College Division, having separated from the University Division in 1957. The won the championship by defeating the .
Seventeen teams were selected to participate, divided into four regions. Three regions consisted of four teams, while the West Region had five. Each region completed a double-elimination round, with the winners advancing to the finals. The finals, made up of the four regional champions, also competed in a double-elimination format.