His Cambodian People's Party (CPP) won a landslide victory in an election on Sunday, taking 82 percent of the vote.
"I would like to ask for understanding from the people as I announce that I will not continue as prime minister," the 70-year-old said in a special broadcast on state television.
The government hailed the 84.6 percent turnout as evidence of the country's "democratic maturity".
Under Hun Sen, Cambodia has tacked close to Beijing, benefiting from huge Chinese investment and infrastructure projects.
China welcomed Sunday's election, with President Xi Jinping sending Hun Sen a personal message of congratulation.