Four charities – Christian Aid, Mercy Corps, Sciaf and Tearfund – will split the funding, receiving £125,000 each.
The charities will be tasked with giving out food packages, improving water access, training hygiene promoters and providing cash transfers.
They will operate in South Sudan, Kenya and Ethiopia as the region faces its driest conditions in decades.
Scotland’s international development minister Neil Gray said: “This funding will support four essential projects ensuring people suffering from the drought receive necessary food supplies and enhanced access to clean water – a vital measure in preventing waterborne diseases.
“The Scottish government is committed to fulfilling its role as a responsible and compassionate global citizen and this aid from our Humanitarian Emergency Fund will provide essential help to those in desperate need.”