"The president... decrees: Lassina Zerbo is named prime minister," government spokesman Stephane Wenceslas Sanou said, reading the decree on television.
Zerbo, 58, was executive secretary of the Vienna-based Comprehensive Nuclear-Test-Ban Treaty Organisation (CTBTO) from 2013 until this summer.
He will take over from Joseph Dabire, whose resignation Kabore accepted on Wednesday as he sought to defuse anger over the government's perceived inability to stamp out jihadist violence in the country.
A new cabinet line-up is expected in the coming days.
Jihadist attacks have grown increasingly regular and deadly in Burkina Faso since 2015, killing 2,000 people and displacing 1.4 million from their homes, especially in the north and east.
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