Kirk Woodman was abducted by gunmen on Tuesday night from a mine exploration camp in the country’s northern region.
Canada’s Foreign Minister Chrystia Freeland condemned those responsible “for this terrible crime”.
Mr Woodman was the second Canadian to go missing in Burkina Faso in recent weeks.
Ms Freeland said that Canada is working with the Burkina Faso government and other international partners “to pursue those responsible and bring them to justice. The government’s priority is the safety and security of Canadians”.
So far, little is known about the circumstances surrounding Mr Woodman’s kidnapping from the camp, located near the Niger border, by unidentified individuals and his death. No group has taken responsibility.
Islamist militants have established a presence in northern Burkina Faso in recent years, carrying out attacks in the region and far beyond.
The country recently declared a state of emergency in some of its northern provinces.
Burkina Faso is one of the countries that make up Africa’s Sahel region, which is home to a number of Islamist groups, some aligned with al-Qaeda.
Burkina Faso’s Foreign Ministry released a statement on Thursday saying an investigation had been opened into Mr Woodman’s death and that all measures are being taken to find those responsible.
It said the body of the Canadian geologist was found on Wednesday near the country’s borders with Mali and Niger in Gorom Gorom.
A spokesman for Burkina Faso’s security ministry told AFP that Mr Woodman was found dead of gunshot wounds.
Mr Woodman’s family released a statement to the media thanking people for their messages of support and asking for privacy.
“Kirk was a loving and hardworking husband, father, son and brother,” the family said.
“Not a day will go by that he won’t be missed”.
Mr Woodman, from Halifax, Nova Scotia, was vice-president of exploration at Progress Minerals and had 20 years experience working in West Africa.
Company CEO Adam Spencer said in a statement that they were “heartbroken by the tragic loss”, and called his former colleague “a kind person, a dedicated father and husband”.
Canadian and Italian still missing
A pair of aid workers also went missing in Burkina Faso last month.
Canadian officials have told media they are treating the disappearance of Canadian Edith Blais, 34, and Italian Luca Tacchetto, 30, as a kidnapping.
The two were last heard from on 15 December in the city of Bobo-Dioulasso in south-western Burkina Faso. Family members say the pair were supposed to travel to neighbouring Togo together for a humanitarian aid mission, but never arrived.
Canada warns its citizens to avoid all non-essential travel to Burkina Faso due to the threat of terrorism, and to avoid travel completely in northern Burkina Faso up to the Mali and Niger border “due to the threat of banditry and kidnapping”