Munteanu, who has served as prime minister since November 2025, gave no full explanation for his decision.
"Today, my term as prime minister comes to an end," he said in a post on X on Friday.
"The moment I realised that I could no longer carry out my mandate in accordance with my principles and convictions, I chose to step down."
The move is a challenge for President Maia Sandu and her ruling pro-European Party of Action and Solidarity (PAS), now in its second consecutive term.
According to Moldova's parliamentary procedure, Sandu will hold consultations with parliamentary groups and then nominate a candidate for prime minister.
Munteanu, 62, was appointed following a parliamentary election in September 2025 in which PAS resoundingly defeated a Russia-leaning rival and won a fresh mandate to pursue Moldova's European Union drive.
Before that, he worked outside Moldova for some 20 years including for the World Bank.
"I will continue to serve my country from whatever position I may hold," he said.
Moldova, nestled between Ukraine and EU member Romania, is a candidate for EU membership.
It has a Romanian-speaking majority and a large Russian-speaking minority, and political power has oscillated for decades between parties supporting closer ties with Europe and those seeking better relations with Moscow.
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