Before taking the Princeton job in 2011, he served as an assistant for the Northwestern Wildcats men's basketball team for 11 seasons under Bill Carmody.

[4][11] The Tigers entered the 1998 NCAA Division I men's basketball tournament on a 19-game winning streak and finished the season ranked eighth in the final USAToday/NABC Coaches Poll.

[18] In the 1998 tournament opening game for the fifth-seeded Tigers, he scored 19 points to help them defeat the UNLV Runnin' Rebels 69–57, which marked the team's 20th consecutive win—a school record.

Carmody used Henderson, who commonly scrimmaged with the players, as part of a joke for a Sports Illustrated: "I don't mind that Mitch is cagier and smarter than all those guys on the court.

He inherited a 2010–11 team that narrowly lost to Kentucky in its opening game of the 2011 NCAA Division I men's basketball tournament.

[30] Eventually, Princeton earned its first home win against a ranked opponent since the 1976–77 team's January 3, 1977 victory over Notre Dame by defeating Harvard (No.

[32][33] Princeton also defeated eventual 2012 ACC men's basketball tournament champion Florida State five weeks after Harvard did.

Evbuomwan was surrounded by a supporting cast of All-Ivy League honorees, including first-teamer Jaelin Llewellyn, and second-team Ethan Wright.

Senior and returning Ivy League Player of the Year, Tosan Evbuomwan, garnered MVP honors in his home country.

[49] On January 7, 2023, Henderson won his 100th Ivy League game as head coach at Princeton, beating the Cornell Big Red, 75–68, in Ithaca, NY.

He is the second head coach in the history of Princeton men's basketball to win 100 league games; Carril was other to reach that threshold.

[50] In March 2023, Henderson guided the 2022–23 Princeton Tigers into the Sweet 16 of the NCAA D1 men's basketball tournament with wins over #2 seed, Arizona, and #7 Missouri.