She is now on day five of her week-long tour of Africa.
She and her local counterpart Margaret Kenyatta held talks on the welfare of mothers and children, and conservation, according to the Kenyan presidency.
Malawi has received a total of 9.6 million textbooks in the past few years through a US-funded national reading programme.
"Meeting those children and understanding their different way of life is why I wanted to travel here", Trump said.
The White House said Malawi was chosen because of the high poverty rate and the difficulties children-especially girls-have in accessing education. Another sign reportedly referenced President Trump's notorious remark about "s***hole countries."
Melania Trump briefly lost her footing when a baby elephant startled her with a sudden move, but the first lady was anything but out of step when children at an orphanage welcomed her to their home with African song and dance.
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Trump greeted two administrators as she arrived at the school with Virginia Palmer, the USA ambassador to Malawi.
The first lady was similarly immersed in the moment earlier at Nairobi National Park, where she had gone early Friday to highlight elephant conservation. As CNN reporter Kate Bennett tweeted, a small group of protesters - who may or may not have been Americans living near the US embassy - held up signs with #MeToo-inspired slogans as Trump drove past.
Beyond hosting first ladies at the White House or meeting with them at the United Nations, it is unclear how much Trump knew about Africa before she made a decision to visit. "I was heartened to spend time with the students and was honoured to donate school supplies and soccer balls".
US First Lady Melania Trump receiving flower on her welcome to Kenya at the JKIA. The people love her, and she loves them! Just 77 teachers educate more than 8,500 students who attend the school. The sounds of women ululating were heard at each of her public appearance.
Mrs Trump also plans to visit the State House to meet over tea with Malawi's first lady Gertrude Mutharika.