Just one week after losing the Wimbledon final to Novak Djokovic, Federer landed in the capital Lilongwe.
The world's number two player is on Monday scheduled to open a childcare centre to improve early childhood development.
"I have always thought children are tomorrow's future and I really enjoy supporting them and giving them an opportunity to be able to go to school," Federer told AFP on arrival at the airport.
Working with international charity Action Aid, Federer's foundation has been working in six districts in Malawi since 2011 and aims to reach 135,000 children by 2021.
"I think it's really important that every child should have this opportunity, so I am trying to help as much as I can," he said.
Child malnutrition is a pressing issue in Malawi, where more than half of children aged between 18 and 23 months suffer from stunted growth, according to a recent study.