The foreign ministry's announcement declaring Ambassador Kim Hak-Chol "persona non grata" came as the UN Security Council unanimously imposed new sanctions on North Korea for its sixth and largest atomic test that took place early this month.
It also followed a decision by Mexico last week to expel the North Korean ambassador on its territory.
Peru's foreign ministry statement said the decision was made given North Korea's "repeated and flagrant violation" of previous UN Security Council resolutions, which "constituted a serious and unacceptable threat to international peace and security, as well as stability in northeast Asia and in the world."
It called on Pyongyang to "respect international law and to put an irreversible and verifiable end to its nuclear program."
The Peruvian foreign ministry noted that in March, it had ordered North Korea to halve the number of diplomats in its Lima embassy, from six to three.
The moves by Peru and Mexico followed came after US Vice President Mike Pence urged them, along with Brazil and Chile, to break off diplomatic relations with North Korea. (AFP)