After playing for Ownie Carroll at Seton Hall, Sheppard coached high school baseball. He became the head coach at Seton Hall after Carroll retired at the end of the 1972 season. In Sheppard's first seven seasons, the Pirates played in six NCAA Tournaments and two College World Series. The team went 22-8 in his first season. It reached the District 2 Regional, where it lost consecutive games to Penn State and Temple. In 1974, Seton Hall went 3-0 in the District 2 Regional to reach the College World Series, where it lost to Southern Illinois, 5-1, and Texas, 12-2. In 1975, the team returned to the College World Series, where it went 1-2 with an elimination-game win over Florida State. The Pirates also qualified for NCAA Tournaments in 1976, 1977, and 1979, reaching the Northeast Regional final against Maine in 1976. Future major leaguers Rick Cerone and Dan Morogiello played for Sheppard during the 1970s. Seton Hall appeared in the NCAA Tournament three more times in the 1980s. Their deepest run came in 1984, when they again lost to Maine in the Northeast Regional final. The program began competing the Big East Conference in 1985. In its first six seasons in the conference, it won the South Division five times and played in the Big East Tournament five times. It won the tournament in 1987. Sheppard was named Big East Coach of the Year in 1985, 1987, and 1989. Several notable players played for Sheppard in the 1980s: John Morris, Tony DeFrancesco, Pat Pacillo, Rich Scheid, Craig Biggio, John Valentin, Kevin Morton, and Mo Vaughn. In the 1990s, Seton Hall won a regular-season conference championship in 1990 and placed second multiple times but failed to qualify for an NCAA Tournament. Its highest win total came in 1995, when the team went 38-16. Future major leaguers Mike Moriarty, Matt Morris, and Jason Grilli played for Sheppard during the decade. In 2000, Seton Hall returned to the NCAA Tournament. The Pirates went 36-14 in the regular season. They lost in the Big Eastchampionship game, but received an at-large bid to the 2000 NCAA Tournament. As the third seed in the Columbia Regional, they went 0-2, losing games to second-seeded Wake Forest and fourth-seeded Liberty. Sheppard missed the entire 2001 season while recovering from triple-bypass surgery. His son, Rob, served as interim coach during the season. Sheppard returned for two seasons but resigned following the 2003 season in controversial circumstances. In March 2003, Steve Politi of the Newark Star-Ledger published an article in which former players and their parents accused Sheppard, an ex-Marine, of using harsh punishments and racial slurs. Others, including other former players, fellow coaches, and media members, defended Sheppard and argued there was no proof of such behavior. Seton Hall conducted a confidential investigation of the incident, the results of which were not published. Sheppard resigned in summer 2003; the university's press release about his resignation cited "health reasons and a desire to spend more time with his children and grandchildren." Including games during the 2001, when his son Rob served as interim head coach, Sheppard retired with 998 career victories. Rob served as Seton Hall's interim head coach in 2004 before being named to the position permanently for the 2005 season.
Head coaching record
Below is a table of Sheppard's yearly records as a collegiate head baseball coach.
