Holloway, the university's the first Black president, will take a year-long sabbatical and then become a Rutgers professor.
He told the Star-Ledger that political climate surrounding universities ultimately drove his decision.
He raised concerns about constantly needing security for himself and his family in public.
Holloway is the university's 21st president and helped lead the school to increased enrollment and alumni support since taking over in 2020.
"I remain steadfast in my belief that Rutgers is on the rise and is earning the respect it has long deserved," he said. "I look forward to seeing it flourish in the years ahead."
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