Knut Ostby, who has served as a UN resident coordinator for more than 11 years, replaces Renata Lok-Dessallien in his new role, the UN said in a statement.
The announcement comes after more than 600,000 minority Rohingya Muslims have been driven out from Myanmar since late August amid a brutal crackdown by military security forces in northern Rakhine state.
International humanitarian assistance, the UN and international media have not been allowed to enter the region, amid allegations of human rights abuses.
The UN statement said Lok-Dessalien will take another assignment at UN headquarters. UN Secretary-General Antonio Guterres said he was "grateful" for Lok-Dessallien's "important contribution and service" to the UN's work in Myanmar.