A government spokesperson did not immediately say why it had labeled Manzi, the U.N.'s resident coordinator in Burkina Faso, "persona non grata" and demanded that she leave on Friday.
A spokesperson at the U.N. headquarters did not immediately respond to a request for comment.
Burkina Faso, one of the world's poorest countries, is in the grips of an Islamist insurgency in which militants linked to al-Qaeda and Islamic State have killed thousands of civilians and created one of the continent's fastest-growing humanitarian crises.
Nearly 2 million people have been displaced and reside in makeshift camps, many run by the United Nations, along the arid countryside.
The violence, which has rumbled on for about seven years, has been focused in the north and east, crippling local economies, causing mass hunger and restricting the access of aid organizations.
The U.N. provides some essential services, including supplying food for thousands of malnourished children.
Manzi, who has long experience in humanitarian activities in developing countries, was appointed to the post in Burkina Faso last year.