The region, particularly Kenya, Somalia and Ethiopia, has been lashed by unrelenting downpours since the beginning of the month due to the El Nino weather phenomenon, inundating homes and farmland.
About 46 people had died in Kenya, 32 in Somalia and another 33 in Ethiopia, Save the Children said, warning the rains were "showing no signs of slowing down".
The Horn of Africa is one of the regions most vulnerable to climate change and extreme weather events are occurring with increased frequency and intensity.
The region is emerging from the worst drought in four decades after multiple failed rainy seasons that left millions of people in need and devastated crops and livestock.
"Heavy flooding and displacement have cut off families and children from basic services including access to food, healthcare, water and hygiene services," said Xavier Joubert, Ethiopia director for Save the Children.
"With that comes the real risk of waterborne diseases including cholera and measles."
Humanitarian groups have warned that the situation is only likely to worsen and called for urgent global intervention as El Nino is expected to last until at least April 2024.
El Nino is typically associated with increased heat worldwide, as well as drought in some parts of the world and heavy rains elsewhere.
Between October 1997 and January 1998, devastating floods caused by El Nino led to more than 6,000 deaths in five Horn of Africa countries.
At least 1,800 people died in Somalia where the Juba River burst its banks.
At the end of 2019, 265 people died and tens of thousands were displaced during two months of relentless rainfall in several countries in East Africa.
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