Haiti has suffered from decades of instability but the situation escalated in February when armed groups launched coordinated attacks in Port-au-Prince to overthrow then-prime minister Ariel Henry.
Gangs currently control 80 percent of the city, where MSF said the medical needs are "immense."
"MSF is now resuming activities thanks to a constructive dialogue with key stakeholders and involvement by the authorities to ensure respect for our teams and our medical mission," the non-governmental organization said in a statement.
But the group said it would not resume patient transports, as "the risk for our teams and patients remains high, particularly in ambulances."
Three MSF-run hospitals and a clinic in the greater Port-au-Prince metropolitan area will reopen, but the Turgeau hospital will remain closed, due to the issue with patient transports, it said.
MSF suspended operations on November 19 over what it said was "violence and threats from police," after two patients were shot dead.
"These past three weeks have been especially painful," Jean-Marc Biquet, MSF's head of mission in Haiti, said in a statement.
"Despite the commitments made by the authorities, the risks remain high, and our ability to continue our work in Haiti is uncertain as we move ahead," he said.
"We call on all parties to respect our medical and humanitarian mission so that we can respond to medical needs to the full extent of our capacity."
Nearly 200 people were killed in brutal violence in Port-au-Prince last weekend, reportedly orchestrated against voodoo practitioners. The government has condemned a massacre of "unbearable cruelty."
The latest killings bring the death toll this year in Haiti to around 5,000 people, according to the United Nations.
