MSF said a blast “partially destroyed” a hospital at Abs, located in the rebel-held province of Hajja, in the fourth attack on one of its facilities in less than a year.
The United States and Amnesty International separately condemned the attack.
Nine people were killed in the explosion, including one MSF staff member, while two more patients died while being transferred to another clinic.
“Once again, a fully functional hospital full of patients and MSF national and international staff members, was bombed in a war that has shown no respect for medical facilities or patients,” Teresa Sancristoval, of MSF’s Emergency Unit in Yemen, said in a statement.
The GPS coordinates of the hospital “were repeatedly shared with all parties to the conflict, including the Saudi-led coalition, and its location was well-known,” the statement added.
The coalition has been battling Iran-backed rebels since March 2015 in support of Yemen’s government, after the insurgents seized Sanaa before moving into other parts of the country.
Earlier this month, the coalition acknowledged “shortcomings” in two out of eight cases it has investigated of UN-condemned air strikes on civilian targets in Yemen.
On Monday, it promised to probe another attack that MSF said killed 10 children over the weekend at a school in the rebel-held northern province of Saada.
The UN says that more than 6,400 people, mostly civilians, have been killed in Yemen since last March.