WASHINGTON—President Trump is replacing the acting IRS commissioner that he appointed just three days earlier, continuing the upheaval at the top of the tax agency, according to people familiar with the matter.

Treasury Secretary Scott Bessent appointed his deputy, Michael Faulkender, as the next acting commissioner of the Internal Revenue Service after reports the current leader of the agency, Gary Shapley,

Gary Shapley, whom President Donald Trump named acting commissioner of the Internal Revenue Service earlier this week, will no longer serve in the role, according to a White House official and a source briefed on the matter.