Merino, 59, stepped down shortly after a crisis session of Congress called on him to quit power before 6:00 pm (2300 GMT) or face censure.
“I want to let the whole country know that I’m resigning,” Merino said in a televised address, a day after a police crackdown on protesters left at least two people dead.
Congress is expected to appoint a new president-- the South American country’s third in a week.
Thousands have taken to the streets in days of protests against Merino following the ouster of his predecessor Martin Vizcarra, who was impeached on corruption allegations on Monday.
Elections are scheduled for April 2021 and Merino was scheduled to leave power in July, when Vizcarra’s mandate was to end.