Kernen began his head coaching career for his alma mater, San Gorgonio High School, spending two years with the program from 1975 to 1976 before moving up to the junior college level as pitching coach at Orange Coast College in 1977. From 1977 to 1982 and again in 1987, Kernen was pitching coach at Cal State Fullerton under Augie Garrido. Kernen helped to turn the Titans into a perennial postseason contender winning the Big West Conference 5 straight seasons, including trips to the College World Series in 1979 and 1982, with the Titans winning the national championship in the 1979 season. During his time at Fullerton, he coached 14 pitchers who were selected by Major League Baseball in the amateur draft, four of whom reached the big leagues in Gary Buckles, Larry Casian, Jeff Robinson, and No. 1 draft pickMike Harkey. Following his father's passing, Kernen left the Titans after the 1982 season to manage his family's business and returned to Cal State Fullerton for the 1987 season. In 1988, Kernen followed Garrido to Illinois.
Cal State Northridge (1989–1995)
Kernen's first major college head coaching position was at Cal State Northridge, where he led the Matadors from 1989 to 1995 in their transition from Division II to Division I. The Matadors, who had been successful at the Division II level, having won national titles in 1970 and 1984, transitioned to Division I under Kernen's auspices. 1990 was the last year of Division II play for the Matadors, and in this final year Kernen guided the team to the NCAA Division II College World Series title game. This effort earned Kernen the Division II West Region Coach of the Year honors. In 1991, the first year of Division I play for the Matadors, Kernen led CSUN to a 44–18–1 record, the West Regional championship game and a #10 ranking in the final NCAA Division I poll, only the second time in NCAA baseball history a first year team finished in the Top 10, the other being Augie Garrido's Cal State Fullerton team in 1975. In seven seasons with the Matadors, Kernen's record was 240–154–3. In August 1995, Kernen resigned from Cal State Northridge to pursue a career in theater in New York City. He studied dramatic writing at Columbia University in 1995 and 1996. At Cal State Northridge, several future college head coaches worked under Kernen. Rick Vanderhook, who was an assistant coach from 1989 to 1990, has been head coach at Cal State Fullerton since 2012. Jody Robinson, an assistant on the 1991 team, was head coach at Loyola Marymount from 1992 to 1996. Following one season on staff in 1992, Stan Sanchez has been head coach at Southern Colorado since 1993.ref name="CSU Pueblo"> Mike Batesole, an assistant from 1994 to 1995, was head coach at Cal State Fullerton from 1996 to 2002 and has been head coach at Fresno State since 2003.
NC State and Cal State Fullerton assistant (2002–2007)
Kernen returned to coaching in the 2002 season, hired in September 2001 as pitching coach at NC State under Elliott Avent. He left a week before the 2003 season. In 2007, Kernen returned to Cal State Fullerton, this time as a volunteer assistant coach on a team that made the College World Series.
Cal State Bakersfield (2009–2015)
hired Kernen to be its inaugural baseball head coach in May 2007. He put together a roster of 25 for the program's debut season in 2008 entirely from freshmen and junior college transfers. In its debut season of 2009, Cal State Bakersfield defeated defending College World Series champions Fresno State three out of five times to become the first-ever first-year Division I baseball team to defeat a defending national champion. On March 7, 2011, Cal State Bakersfield received its first ever national ranking, at no. 30 on the Collegiate Baseball poll. After four seasons as a Division I independent, Cal State Bakersfield joined the Western Athletic Conference beginning in the 2013 season and won the regular season title that year, for which Kernen won WAC Coach of the Year honors. On May 8, 2014, Kernen announced that he would retire after the season. Kernen reversed course three weeks later and decided to remain as head coach on a year-by-year basis. In his final season as head coach, Cal State Bakersfield made the NCAA Tournament and won the WAC Tournament title for the first time in program history. Cal State Bakersfield went 1–2 in the tournament, including a 2-1 win that eliminated 2014 College World Series participant Ole Miss from the tournament. On August 31, 2015, Cal State Bakersfield promoted assistant coach Bob Macaluso to be head coach. Macaluso went 19–37 in his only season as head coach before being fired in December 2016. During Kernen's seven seasons, Cal State Bakersfield went 197–198–1 and produced 15 players selected in the Major League Baseball Draft.
Head coaching record
Below is a table of Kernen's yearly records as an NCAA head baseball coach.
Theatre career
After coaching at Cal State Northridge, Kernen left college baseball to pursue a career in theatre and film. He was accepted into the dramatic writing program at Columbia University in New York City. As a playwright, Kernen produced multiple plays. In 1997, Kernen wrote and produced And Other Fairy Tales and A Graveyard Symphony; in the next years, Kernen followed these with the more ambitious Galleria degli Angeli and Musica de Mariposa. And Other Fairy Tales was honored as a finalist in the Oglebay Institute National Playwriting Competition. Kernen produced, wrote and directed a short film in 2006, In the House of Athazagora. Following his retirement in 2015, Kernen returned to New York City to resume his theatre/film career. He is currently on pre-production for a feature film based on his play Galleria degli Angeli.