The speculation followed reports that Bongino had a heated exchange with Attorney General Pam Bondi over her handling of the Epstein Files release.
Bongino reportedly did not show up for work on Friday, which further fuelled the rumours of his departure.
The Justice Department's memo confirmed Jeffrey Epstein died by suicide and had no “client list”, which disappointed some conservative figures expecting more disclosures.
Both Trump and the White House denied the resignation claims, with Trump also expressing strong support for Pam Bondi's performance.