The US First Lady then visited Chipala Primary in Malawi's capital, Lilongwe.
President Trump supported his wife's visit, sharing that, "It is a handsome thing to see".
A statement to newsrooms from the Presidential Strategic Communications Unit (PSCU) said Mrs Trump, who landed on Thursday night, will first visit the David Sheldrick Wildlife Trust accompanied by her Kenyan counterpart Margaret Kenyatta.
Her first African tour since her husband became president of the United States, Melania has taken her "Be Best" campaign to Africa.
She's focusing the trip on her interest in child welfare.
However, Phiri said the protesters could have done better, observing that the timing of their actions did not tally with the work the USA first lady came to do in the country.
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Despite the protests, President Trump praised Melania for her five-day solo tour of Africa, saying: "Our country's great First Lady, Melania, is doing really well in Africa". Mrs. Trump sat in a rooftop garden and watched performances by dance groups representing different regions of Malawi. To say her visit didn't get off to a warm start would be an understatement. "Thank you for educating them to "be best" and to grow up into educated adults for generations to come".
"I was heartened to spend time with the students and was honoured to donate school supplies and soccer balls", she said.
Following the school visit, Trump arrived at the statehouse, home to Peter Mutharika, the President of Malawi, at 4:17 pm.
On her first day in Ghana, Trump visited a baby clinic and toured Greater Accra Regional Hospital and a new facility where she passed out teddy bears and spent time with the children.
And two other white people had a "welcome to Malawi # notashithole!" sign.