He served as head coach of the Ohio Bobcats men's basketball team for seven years (1980–1986), where he helped rebuild the program which had suffered through several losing seasons, and helped lead the team to two MAC Tournament titles (1983 and 1985), two NCAA Tournament appearances (1983 and 1985), and one National Invitation Tournament appearance (1986).
University of Nebraska
Following Nee's tenure at Ohio, he became the coach of the Nebraska Cornhuskers from 1986 to 2000. Nee took a historically lackluster Husker program to the next level, leading Nebraska to five NCAA Tournament appearances from 1991–1994 and in 1998. They won the Big Eight Tournament Championship in 1994. His 1996 squad won the NIT Championship. Nee was fired in 2000 by then athletic director Bill Byrne.
After Nebraska, Nee then went to Robert Morris University for one year and then became head coach of Duquesne University's Duquesne Dukes, in the spring of 2001. Nee officially resigned as head coach after the season's final game on March 4, 2006. Nee then joined the basketball staff at Rutgers University in September 2008. In 2009 Nee left Ohio to join the staff at Towson University.
United States Merchant Marine Academy
On October 4, 2010 Danny Nee was named Head Men's Basketball coach at the United States Merchant Marine Academy.