US President Joe Biden said he awarded Mr Ejeta the medal for his "outstanding contributions to the science of plant genetics".
Mr Ejeta is acclaimed as one of the world's leading plant geneticists.
He specialises in the study of sorghum, a popular source of food in Africa.
In 2009, Mr Ejeta won the prestigious World Food Prize for developing a sorghum hybrid that is resistant to both drought and the parasitic weed Striga, which commonly invades farms in Africa.
Sorghum is the fifth-most important cereal crop globally - after maize, wheat, rice and barley.
It is also the second-most important cereal in Africa and has been embraced as a staple by several countries on the continent, particularly those prone to drought.
Mr Ejeta was raised in a single-roomed thatched home in a village in central Ethiopia not far from the capital, Addis Ababa.
However, he had limited access to school and had to travel 20km (12 miles) to a nearby town to attend lessons, only returning home at weekends.
His childhood, which was plagued by hunger and food scarcity, has heavily influenced his scientific research over the years, fuelling him in his pursuit to improve food security.
He mentioned experiencing hunger as a child in one of his interviews with the BBC.
He added that going to school in the morning "with an empty stomach is a challenge. So I have experienced hunger on a regular basis".
The president of Purdue University in the US state of Indiana, where Mr Ejeta works as a professor and leads global food security programmes, celebrated the award, hailing Mr Ejeta as "a role model of perseverance" and "one of the most impactful geneticists in the world".
Mr Ejeta, who holds American nationality, was one of nine leading US scientists awarded at the White House by President Biden on Tuesday.
The National Medal of Science has been awarded by US presidents since 1959 to "individuals deserving of special recognition for their outstanding contributions" in various science-related fields.
Mr Ejeta also received the National Hero Award from the Ethiopian government shortly after he won the World Food Prize in 2009, the highest national honour bestowed on Ethiopian citizens.
He was also appointed to the Board for International Food and Agricultural Development in 2011 by then US President Barack Obama.
Source: www.bbc.com
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