He was the interim men's head basketball coach at the University of Texas at El Paso (UTEP).

[7] Johnson then became an assistant at Arizona under Lute Olson for five seasons from 1993 to 1998, including the 1997 national championship team.

San Jose State athletic director Chuck Bell stated: "While recognizing that the fan's verbal harassment of Coach Johnson throughout the game led to the confrontation, under no circumstances can a coach allow himself to be placed in a situation that jeopardizes the safety of the players and the fans in an arena.

"[13] The same day of the reprimand, the San Jose Mercury News revealed that Johnson had a suspended driver's license due to three arrests for drunk driving from 2002 and 2003.

[15] In 2008, the NCAA reduced the number of scholarships for San Jose State men's basketball by two, as a result of an unsatisfactory four-year Academic Progress Rate of 886 (the minimum satisfactory APR is 925) that spanned Johnson's final two seasons (2003–04 and 2004–05) and the first two seasons of succeeding head coach George Nessman (2005–06 and 2006–07).

On February 24, 2011, Johnson was ejected from UTEP's game at East Carolina for receiving two technical fouls.

[18] On January 30, 2015, C-USA issued a reprimand to Johnson for throwing a piece of paper on the court during UTEP's game against Marshall.

On November 28, 2017, Johnson was named interim head coach of the Miners following Floyd's abrupt retirement.