The pop star was welcomed with song and dance from youngsters at the Home of Hope, from where she adopted David Banda in 2006.
She said she was pleased to visit the orphanage, in the western district of Mchinji near the Zambian border.
'I'm happy that David is back to see his brothers and sisters,' she said.
David, now eight, was accompanied by his sister Mercy James, also eight and adopted from Malawi, and Madonna's natural children, Rocco and Lourdes.
The visit saw him taken to see his former crib, which has been preserved in his memory.
It was not known if the family would also visit the Kondanani Children's Village, where Madonna adopted Mercy in 2009 after a protracted court battle.
The singer arrived in Malawi on Monday to visit projects she has supported.
She had initially planned to build a $15m (£10m), 500-bed Raising Malawi Academy for girls, before changing plans to help fund several community schools.
Meanwhile, the singer expects to raise more than $5m (£3.3m) to support education for girls in Afghanistan, Pakistan and other countries by selling an abstract French painting she has owned for more than 20 years.
From Associated Press Via Yahoo! News