The missile struck the medical facility in the Razeh district of Saada province, according to communications officer Malak Shaher.
She said MSF could not specify whether the centre was hit in an air strike by the Saudi-led coalition or by a rocket fired from the ground.
Saada is the heartland of the Iran-backed Shiite Huthi rebels that the coalition has been bombing since March in support of Yemen's beleaguered government.
MSF last month accused the coalition of bombing its clinic in Taez, southwest Yemen, where nine people were wounded including two agency staff.
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The UN envoy for Yemen Ismail Ould Cheikh Ahmed arrived today in Sanaa in a bid to convince the rebels and their allies to attend fresh peace talks slated for next week.
But Foreign Minister Abdel Malak al-Mekhlafi told AFP yesterday that the talks will not take place until January 20 at the earliest.
The government met the rebels and their allies in Switzerland last month for six days of talks that ended with no major breakthrough.
In Yemen's second city of Aden Sunday, intelligence colonel Ali Saleh al-Nakhibi was shot dead by unknown gunmen, a security official said.