A military guard of honour and groups performing traditional dances, chanting and beating drums welcomed her at Kamuzu International Airport.
Clinton met with President Joyce Banda, Africa’s second woman leader after Liberia’s Ellen Johnson Sirleaf, at her official residence State House.
The two exchanged warm words.
“For a long time, we have been women and children activists. I have been waiting for the day when we would meet,” Banda told Clinton as the two held hands.
Clinton next sped off for a short trip to the US embassy.
She travelled from Kenya, where she met with presidents from Kenya and Somalia as part of a marathon eleven-day Africa tour that started in Senegal.
She was due to fly to South Africa later on Sunday, where she would meet with anti-apartheid icon and Nobel Laureate Nelson Mandela.
A State Department spokeswoman confirmed Clinton tagged visits to Nigeria and Benin onto the trip after South Africa. She is also expected in Ghana for the the state funeral of late president John Atta Mills.
Banda was sworn in as president in April following the death of late president Bingu wa Mutharika.
She swiftly set about restoring relations with foreign donors, who had suspended funds due to concerns about hardline governance and rights issues under Mutharika.
In June the US said it would restore aid worth $350 million to Malawi’s energy sector in light of Banda’s “bold actions” to reform the government.