It has caused the worst drought in more than 30 years in Ethiopia, Unicef said.
Its effects could also be "particularly harsh" in Somalia, amid fears of flooding, it warned.
El Nino is caused by Pacific Ocean warming.
"The weather phenomenon, among the strongest on record, is likely to cause more floods and droughts, fuel Pacific typhoons and cyclones and affect more areas if it continues strengthening as forecast over the coming months," Unicef said in a statement.
It said 8.2 million people in Ethiopia faced food insecurity, while an estimated 350,000 children needed treatment for severe acute malnutrition.
"To make matters worse, the weather phenomenon may also bring flooding to some areas of the country in the coming months," Unicef said.
Ethiopia says it has food surpluses in country which it continues to send to areas affected by the drought.
"The government is working hard to ensure that no-one dies from lack of food in this El Nino year and, contrary to some Western news reports, there will not be famine of any sort, let alone anything remotely like the magnitude of that of 1984," a statement from the Ethiopian embassy in the UK said.
Unicef said severe flooding was also expected in neighbouring Somalia, where more than three million people were in need of aid as the effects of El Nino were already being felt.
In Kenya, the government estimated that 2.5 million children may be affected by floods, landslides, mudslides and diseases linked to the El Nino rains, it said.
In southern Africa, Zimbabwe, Malawi and South Africa have been hit by a drought.
"In Malawi, where almost half the children are already undernourished, Unicef fears the worst drought in almost a decade could cause a further increase in severe acute malnutrition," it said.
In Zimbabwe, the number of people in need of food aid was expected to reach 1.5 million by the time the January-March "lean season" sets in, Unicef said.
In South Africa, livestock has been dying as a result of the drought, and water restrictions have been imposed in the main city, Johannesburg, and other areas, correspondents say.
Some 11 million children are at risk from hunger, disease and water shortages in east and southern Africa because of the strengthening El Nino weather phenomenon, the UN children's charity has said.