The WFP suspended food distributions in all of Ethiopia in June, a day after the United States announced it was doing the same because of diversions of aid.
Neither WFP nor the U.S. Agency for International Development (USAID) gave details about the aid diversions that led to their decisions.
But an internal briefing by a group of foreign donors, seen by Reuters, said USAID believes food has been diverted to Ethiopian military units as part of a scheme orchestrated by federal and regional government entities.
More than 20 million people need food assistance in Ethiopia, after the worst drought in decades and a two-year conflict in the Tigray region that has killed tens of thousands.
In the last six months, around 35,000 people have fled from Sudan to Ethiopia. Ethiopia hosts a further 850,000 refugees mostly from Somalia, South Sudan and Eritrea.
"Food is a lifeline for refugees living in unimaginably hard conditions, and it's a relief that we now have measures in place to resume vital support," Valerie Guarnieri, WFP's assistant executive director, said in the statement posted on social media platform X on Tuesday.
The WFP had been providing emergency assistance to nearly 6 million people in Ethiopia before it halted its distributions, a decision that was criticized by Ethiopia's government which said it was investigating the claims of theft.
The United Nations agency resumed distributing food aid in parts of the Tigray region in August, but at that stage it was still running test distributions in other Ethiopian regions.
WFP said there had been major reforms at all refugee camps in Ethiopia, with all 24 warehouses in camps now exclusively managed by the WFP.
More non-governmental organizations have been trained to manage food distributions, and new collection procedures will ensure refugees get the right entitlements.