The 1999 NCAA Division III men's basketball tournament was the 25th annual single-elimination tournament to determine the national champions of National Collegiate Athletic Association (NCAA) men's Division III collegiate basketball in the United States.

All sectional games were played on campus sites, while the national semifinals, third-place final, and championship finals were contested at the Salem Civic Center in Salem, Virginia.

[1] Defending champions Wisconsin–Platteville defeated Hampden-Sydney, 76–75 (in two overtimes), in the final, clinching a fourth overall title and a second consecutive championship.

The Pioneers (30–2) were coached by Bo Ryan, who claimed his fourth title at Platteville (1991, 1995, and 1998).

Ryan departed for Division I Milwaukee after this season before eventually becoming the head coach for Wisconsin in 2001.