US Army General John Nicholson traveled to the northern city to meet local leaders and relatives of those who died in the October 3 attack.
A US Air Force AC-130 gunship attacked the hospital run by medical charity Doctors Without Borders in what Nicholson called a "horrible tragedy."
Nicholson's wife Norine accompanied him to Kunduz, along with acting defence minister Masoom Stanekzai.
More than a dozen US military personnel have been disciplined for mistakes that led to the sustained attack. A US military report on the hospital attack is expected to be released within days.
Afghan officials, including Stanekzai, insisted that Taliban fighters, who had overrun the city on September 28, were using the hospital as a base from which to attack Afghan forces. No evidence has been found to support the claims.
Doctors Without Borders, also known by its French initials MSF, immediately ceased operations in Kunduz and has yet to return. The hospital was the only trauma clinic in northern Afghanistan.
Military leaders expect another year of fierce fighting amid uncertainty about the future of the peace process and talks between the Afghan government and the Taliban.
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