The 1999–2000 NCAA Division I men's basketball season began on November 11, 1999, with the Coaches vs. Cancer Classic, progressed through the regular season and conference tournaments, and concluded with the 2000 NCAA Division I men's basketball tournament championship game on April 3, 2000, at the RCA Dome in Indianapolis, Indiana.

Conference tournament winners generally received an automatic bid to the 2000 NCAA Division I men's basketball tournament.

The Mountain West Conference (MWC) began operation in 1999-2000 and its tournament winner did not receive an automatic bid, although UNLV, the winner of the inaugural MWC tournament, did receive an at-large bid.

[84] After eight seasons in which each of Philadelphia Big 5 member played only two games against other Big 5 schools each year, the Big 5 returned to a full round-robin schedule in which each team met each other team once, a format it had used from its first season of competition in 1955–56 through the 1990–91 season.

Temple and Villanova both finished with 3–1 records in head-to-head competition among the Big 5.