The executive director of the World Food Programme (WFP), James Morris, said Zimbabwe's decision would send an important message to other countries in the region which have refused food aid because it might contain GM grain.
Zimbabwe and WFP have agreed that the maize will be milled before being distributed, so that the food aid cannot be planted.
Zimbabwe and some of its neighbours are worried that GM seeds could contaminate locally-grown crops, threatening lucrative exports to Europe, which insists that food must be GM-free.
A Zimbabwean minister says the government has now set up a system of checks to ensure the grain will not enter the eco-system.
Aid
Mr Morris made the announcement after talks in Harare with Zimbabwean President Robert Mugabe.
"The fact that they have now concluded that they are comfortable in accepting GM crops or commodities will be an important signal to other countries in the region," Mr Morris told journalists.
"It will enable us to do our job," he said.
Aid workers say up to 13 million people in seven countries in Southern Africa face famine. In Zimbabwe which was once the bread basket of the region, some six million people are estimated to need food aid.
The WFP says it already has aid pledges for about half of the 600,000 tonnes of food it intends to bring into Zimbabwe in the next few months.
Most of this comes from the United States and is not certified as being GM-free.
The government blames the shortages solely on drought, but the government's campaign to transfer land from large scale commercial white farmers has worsened the situation, say many donors.
Lost markets
The GM row has complicated relief efforts across the region.
Zambia's president is refusing to overturn his ban on GM food aid, labelling it as 'poison' .
Deals to mill GM food before being distributed, so that it could not be planted, have also placated fears in Malawi and Mozambique.
US aid officials deny that the food is unsafe, pointing out that Americans eat GM maize every day.
The World Health Organisation has certified the grain for human consumption and says it does not constitute a danger to people's health.