More than 20,000 people have been affected and "major damage has been seen, notably with homes destroyed and public infrastructure damaged," according to minutes of a cabinet meeting.
Nine were killed, while 12 of the 87 injured were in a serious condition, a statement said.
Communication Minister Ousseni Tamboura, who is also government spokesman, said the victims either drowned or were crushed in unstable dwellings.
The disasters hit one-third of the provinces and 22 towns or cities.
Other Sahel countries also saw torrential rains and floods, such as neighbouring Niger, which has recorded 64 deaths and 70,000 people affected since June.
Tamboura said food, hygiene kits and anti-Covid protection had been distributed in Burkina Faso, as well as funds to help "vulnerable households" repair damage.
The rainy season, from May to mid-October, is often deadly, even when rainfall is moderate, because of poor drainage systems in many homes.
Last year, the government of the former French colony earmarked five billion CFA francs ($9 billion / 7.5 million euros) in emergency funds for flooding victims. Thirteen people died.
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