Manuel Merino’s resignation came amid widespread outrage over the killing of two protesters during pro-Democracy demonstrations on Saturday.
Protesters have taken to the streets for nearly a week over the ouster of ex-President Martín Vizcarra.
The demonstrators allege that Congress staged a parliamentary coup when it impeached Vizcarra on Monday over allegations of corruption.
Merino, the 59-year-old former president of Congress, was appointed interim-leader by legislators on Tuesday.
In a short TV address on Sunday, Merino maintained that Congress acted lawfully when he was sworn into office, but nonetheless said he would be stepping down.
“I, like everyone, want what’s best for our country,” he said.
Congress scheduled an emergency session for Sunday evening to select a new president.
Meanwhile, Vizcarra called on the country’s highest court to step in.
“It can’t be that the institution that got us into this political crisis, that has for five days paralyzed Peru, with deaths, is going to give us a solution, choosing the person who they best see fit,” he said.
With Post wires