Djibo is close to the so-called three-border zone between Niger, Burkina Faso and Mali where jihadist groups are active.
The town has been under siege for almost two years.
"The MSF office was the target of repeated gunfire on Wednesday July 17, 2024 during an attack on the town of Djibo that began at dawn," the NGO said in a statement sent to AFP.
"The building bears visible bullet holes, and medical structures belonging to the Ministry of Health, supported by MSF, and a water distribution site have been vandalised," the NGO said, adding that its teams and patients were unharmed.
MSF was assessing the impact of the attack on its capacity to intervene in the town and said that "local and displaced populations" were the main victims of "insecurity and violence".
MSF condemned the violence and called for respect for humanitarian spaces.
Burkina Faso is governed by a military regime led by Captain Ibrahim Traore, who came to power in September 2022 in a coup.
He has promised to restore security in the country, which has been targeted by jihadists for almost 10 years.
The authorities have not commented on jihadist attacks for months, but regularly claim victories over militants, even though part of the country is still out of the army's control.
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