Holloway, who will be introduced as the Pirates' coach on Thursday, agreed to a six-year deal, sources told ESPN.
"Life has a way of coming full circle," said Holloway, who starred at Seton Hall as a player and later was an assistant coach. "This is certainly a full-circle moment for my family and I. Seton Hall is near and dear to my heart; it's where I became a man, where I met the love of my life, where I spent countless hours honing my crafts as a basketball player and a basketball coach.
"To say that I'm excited to get started as the head men's basketball coach at Seton Hall University would be an understatement."
Holloway, 45, was the breakout coach of this month's NCAA tournament, guiding 15-seed Saint Peter's on a remarkable run. The Peacocks pulled off upset wins over Kentucky, Murray State and Purdue to advance to the Elite Eight, before coming up short against North Carolina.
It was the deepest that a 15-seed has ever gone in the tournament.
"I am incredibly excited to welcome Shaheen Holloway and his family home to Seton Hall," athletic director Bryan Felt said. "Shaheen is a winner in every sense of the word, and he is not only an incredible coach, but also an incredible educator of young men. He works tirelessly to put his student-athletes in a position to succeed, and he makes them believe that they can achieve anything with hard work and determination. That is evidenced by his historic NCAA tournament run this month.
"Shaheen made an unforgettable impact here at Seton Hall first as a student-athlete and then again as an assistant coach, and now we're ready to watch him take over our men's basketball program as head coach and lead our Pirates to further greatness. Welcome home, Coach Holloway!"
Holloway had coached the Peacocks for four seasons, finishing second in the MAAC in both 2020 and 2022. Saint Peter's, considered one of the toughest jobs in the region, won the MAAC tournament this season to advance to the NCAA tournament for the first time since 2011 and only the fourth time in program history.
In four seasons, Holloway went 64-54 overall and 44-32 in league play, winning MAAC Coach of the Year honors in 2020.
Before taking over at Saint Peter's in 2018, Holloway was an assistant coach under Kevin Willard for 11 seasons at Iona and Seton Hall, following Willard from the Gaels to the Pirates in 2010. Seton Hall went to three straight NCAA tournament appearances in Holloway's final three seasons with the program.
Holloway is one of the best players in Seton Hall history, setting the program record for career assists and leading the Pirates to the 2000 Sweet 16. From Queens, he was named to the All-Big East team three times. Holloway also won McDonald's All-American Game MVP honors in 1996 as a high school player.
He replaces Willard, who left earlier this month for the vacancy at Maryland.
"I am ecstatic for Shaheen and his family that they are returning to Seton Hall," Willard said. "I can't think of a better person to take over the program. Shaheen's hard work and determination helped build the foundation of our program and that led to multiple NCAA tournament appearances and a Big East championship. He bleeds Blue and White, and I have no doubt that he will succeed."