"Our teams are resuming activities in the country, with the exception of the Boucle du Mouhoun region where the attack took place," the NGO said in a tweet.
On February 8, armed men targeted a clearly marked MSF vehicle carrying four medics in the northwest of the country, the charity says. Two employees managed to flee but two were killed.
MSF announced the suspension on February 17.
"This measure... was needed out of solidarity with our teams who were in mourning, and to analyze the risks to which we are exposed," it said on Wednesday.
The group said it was focusing attention on Burkina's Centre-North region, "which is facing a security crisis with massive population displacement."
One of the world's poorest nations, Burkina Faso has been rocked by a jihadist insurgency that spilled over from neighboring Mali in 2015.
More than 10,000 civilians, troops and police have been killed, according to an NGO estimate, while more than two million people have fled their homes and around 40 percent of the country lies outside government control.
The country was the scene of two military coups in 2022.
Despite vows by the junta to prevail against the extremists, attacks have escalated since the start of the year, inflicting a death toll currently averaging dozens per week.