The 1961 NCAA University Division baseball season, play of college baseball in the United States organized by the National Collegiate Athletic Association (NCAA) began in the spring of 1961. The season progressed through the regular season and concluded with the 1961 College World Series. The College World Series, held for the fifteenth time in 1961, consisted of one team from each of eight geographical districts and was held in Omaha, Nebraska at Johnny Rosenblatt Stadium as a double-elimination tournament. Southern California claimed the championship.^[1]

This is a partial list of conference champions from the 1961 season. Each of the eight geographical districts chose, by various methods, the team that would represent them in the NCAA tournament. 9 teams earned automatic bids by winning their conference championship while 16 teams earned at-large selections.^[1][2]

The following is an incomplete list of conference standings:

The 1961 season marked the fifteenth NCAA baseball tournament, which culminated with the eight team College World Series. The College World Series was held in Omaha, Nebraska. The eight teams played a double-elimination format, with Southern California claiming their third championship with a 1–0 win over Oklahoma State in the final.^[1]