After graduation, Pikiell stayed on as an assistant for the UConn staff before moving on to
Yale University as an assistant coach from 1992 to 1995. During 1995-96, Pikiell served as the interim head coach at
Wesleyan University. His former coach and colleague
Howie Dickenman then became the head coach for the
Central Connecticut State Blue Devils and hired Pikiell as an assistant coach. He remained from 1997 to 2001, with the Blue Devils reaching the NCAA Tournament in
2000. Pikiell joined fellow UConn alum
Karl Hobbs as an assistant for the
George Washington Colonials from 2001 to 2005, where he was part of the Colonials teams that made the
2004 NIT and
2005 NCAA tournament squads. At the time, Pikiell became the first Connecticut alum who played for Calhoun to coach a Division I program. Taking over a program that transitioned to Division I in 1999, Stony Brook endured three-straight losing seasons in his first three years. In the 2008–09 season, the Seawolves went 16–14 for its first winning season as a Division I program. The following year in
2009–10, Stony Brook earned their first regular season championship with a 22–10, 13–3 record, ending with a semifinal loss in the
tournament. By virtue of winning the regular season, Stony Brook earned an
NIT bid but lost to
Illinois. Pikiell guided the Seawolves to a 15–17 mark in
2010–11, making a run to the
America East Championship game after an upset over top-seeded
Vermont in the semifinals, but lost to
Boston on a last-second foul. From 2011 to 2016, Stony Brook won three America East regular season titles, while winning the conference tournament for the first time in school history in
2016 en route to the Seawolves' first
NCAA tournament appearance. In that span, Stony Brook went 117–47, while appearing in two NIT and two
CBI tournaments in addition to the NCAA Tournament appearance. His overall record at Stony Brook was 192–155 in 11 seasons. During the 2019–20 season, Pikiell led Rutgers to a 20–11 overall record and 11–9 in the
Big Ten Conference. He earned the
Jim Phelan Award for national coach of the year from Colleginsiders.com. On March 14, 2021, Pikiell's Rutgers team was named to the NCAA tournament for the first time since the 1990–91 season. The Scarlet Knights earned a 10 seed in the tournament. On March 19, 2021, Rutgers won its first NCAA tournament game in 38 years, beating Clemson 60–56. This was also Pikiell's first win as a coach in the NCAA tournament. ==Head coaching record==