Mrs Trump landed at Jomo Kenyatta International Airport at around 9pm on her maiden visit to Kenya ahead of her talks with First Lady Margaret Kenyatta on Friday.
A batch of 1.4 million books donated Thursday brought to almost 10 million the total Malawi has received in recent years under USAID's national reading program, officials said.
The school is struggling with only 75 teachers looking after around 8,000 enrolled children.
The U.S. first lady was joyously welcomed at the airport, with singing and dancing by a troupe of women and scores of schoolchildren waving African and Malawian flags.
President Trump supported his wife's visit, sharing that, "It is a handsome thing to see".
US First Lady Melania Trump brought soccer balls and books to a school in Malawi on Thursday to highlight a USAID scheme to support African schools, on the second stop of her four-nation tour of the continent.
She also visited a local traditional ruler, Osabarimba Kwesi Atta II, meeting him in Obama Hall.
At one point, a teacher led the students in a song in English: "We say goodbye but not forever".
However, Phiri said the protesters could have done better, observing that the timing of their actions did not tally with the work the United States first lady came to do in the country.
On Wednesday, she visited a former slave trading fort in Ghana after arriving in Africa from Washington on Tuesday. "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.
And two other white people had a "welcome to Malawi # notashithole!" sign.
The first lady later left Malawi for Kenya.
Mrs Trump is also expected to visit Kenya and Egypt.
The 48-year-old will also tour the Kenya National Theater in Nairobi where she will watch a performance by Sarakasi dancers alongside Margret Kenyatta.