Zida was appointed by civilian interim President Michel Kafondo on Wednesday, but his nomination is a blow to opposition parties, civil society groups, the African Union and France, who have all demanded a swift transition to civilian rule.
The two men met at the presidential palace as soon as the announcement had been made.
Before the appointment, Kafondo told RFI that he believed that the army officer, who was unknown to the Burkinabe public three week ago, “could play an essential role in the stabilisation” of the country and insisted that the army must be involved in the post-Compaoré transition.
Zida earlier dismissed an African Union deadline of two weeks for a return to civilian rule but has pledged to hand over power when the transition is concluded.
That should follow a general election, which may not be before November next year.
Zida has fired the bosses of the national oil and electricity companies, who were both close to Compaoré, accusing them of sabotage and suspended local and regional councils.
Top military officers preferred the 49-year-old second-in-command of the presidential palace to Chief of Staff General Nabéré Honoré Traoré, who claimed the country’s leadership when Compaoré fled.
Zida is a protestant from Yako, in the centre of the country, who went to the commando training centre in Pô in the south and earned a degree in international management at the Jean Moulin University in Lyon, France, before undergoing anti-terrorist training in the US in 2012.
He served in the UN force in the Democratic Republic of Congo in 2008-2009.