"Some 486,000 have been forced to flee within the country, 267,000 of whom in the past three months alone. A further 16,000 are refugees in neighboring countries," the agency said in a statement received by AFP on Friday, Presstv Reported.
All of Burkina Faso's 13 regions now host people fleeing violence, and around 1.5 million people are "in urgent need" of humanitarian aid, it said.
A previous estimate of the number of displaced, given by the Burkinabe government, put the tally at around 300,000.
The impoverished country has been grappling with an extremist revolt since 2015 that began in neighboring Mali.
Combining guerrilla hit-and-run tactics with road mines and bombings, the extremists have killed nearly 600 people, according to a toll compiled by AFP. Civil society groups put the tally at more than 1,000.
UNHCR spokesman Andrew Mbogori, the agency's principal emergency coordinator, issued the statement in Geneva following a visit to Kaya, northeast of the capital Ouagadougou, and to Barsalogho, in central Sanmatenga province.
"Thousands of people are on the move, exhausted and trying to find safety among host families or at transit and official travel sites," the UNHCR said.
"Many have been repeatedly displaced. The prospects for their immediate return to where they come from are poor.
"As a result, their needs and those of host families, already vulnerable by food and nutrition crises in the region, are growing. Women and adolescent girls face particular threats given that health and other essential services are lacking."