David Banda flew via Johannesburg from Malawi overnight with one of the US pop star's bodyguards and her personal assistant and arrived at London's Heathrow airport at around 0530 GMT.
Malawian authorities earlier waived local rules to grant Madonna and her film director husband, Guy Ritchie, an interim adoption, prompting charges from human rights groups that the star used her celebrity status to bypass normal adoption rules.
David Banda, who is leaving behind his father Yohane, will swap his home in a dilapidated orphanage near the Zambian border for a life of luxury in London with one of the world's most famous couples and their two children.
The boy's mother died after she gave birth to him, according to media reports.