The public prosecutor's office in Lisbon said the decision was made after "new indications" emerged during a case review. It gave no further details.
In London, Scotland Yard said the Portuguese prosecutor's decision "follows the discovery of new lines of enquiry as a result of an internal review of their original investigation" by the Portuguese police.
It said the Portuguese investigation will run parallel with British police efforts to find out what happened to the girl who vanished shortly before her fourth birthday during a family vacation in southern Portugal in May 2007.
Portuguese police closed the case in 2008 because authorities had detected no crime. The case sparked global interest because pictures of Madeleine beamed around the world and because her parents were briefly considered suspects before they were cleared and returned home to England.
Madeleine's parents, Kate and Gerry McCann, said in a statement they were "very pleased" about the case being reopened.
"We hope that this will finally lead to (Madeleine) being found and to the discovery of whoever is responsible for this crime," they said.
British detectives have said it's possible that Madeleine is still alive. British police launched Operation Grange in 2011 to try to solve the puzzle about what happened to the girl.
"This is a welcome development, but both sides of the investigation are at relatively early stages, with much work remaining to be done," Scotland Yard said in a statement about its own case and the Portuguese announcement. "This new momentum is encouraging, but we still have a way to go, and as with all major investigations, not all lines of enquiry that look promising will yield results."
British police will travel regularly to Portugal, Scotland Yard added.
Madeleine disappeared from her family's apartment in a resort in Praia da Luz, a coastal town 200 kilometers (120 miles) south of Lisbon, while her parents and their friends were eating dinner nearby.
A team of detectives from Porto, in northern Portugal, began reviewing the evidence in March 2011. British police have also been sifting through the case files in Portugal and say they have identified new avenues of investigation.