Kate and Gerry McCann said Wednesday that Express Newspapers had agreed to pay the equivalent of $1.1 million. The couple's lawyer said the money would go into a fund they have set up to help find their daughter.
Two of the group's newspapers ran front-page apologies Wednesday for suggesting the couple were responsible for Madeleine's death. "Kate and Gerry McCann: Sorry" read identical headlines on the front pages of The Daily Express and The Daily Star newspapers.
The newspapers were among those that went furthest in claiming that the couple were responsible for their daughter's disappearance in front page stories nearly every day.
"We acknowledge that there is no evidence whatsoever to support this theory and that Kate and Gerry are completely innocent of any involvement in their daughter's disappearance," the identical apologies read.
Two further front page apologies were expected to follow in the newspapers' sister publications, The Sunday Express and The Sunday Star.
The McCanns said the Express newspapers had published "numerous grotesque and grossly defamatory allegations" about them.
In a statement read outside London's High Court by spokesman Clarence Mitchell, the couple said they still believed their daughter was alive.
"There is absolutely no evidence that Madeleine is dead or has been seriously harmed," they said.
Weeks after the child's disappearance, Portuguese police named her parents as suspects. The couple say they were not involved in their daughter's disappearance, and they have run an international campaign to find her.
They have complained that they are unable to give their version of events because of Portuguese laws limiting what can be said in criminal cases. But in the meantime British media have published sensational stories claiming to be based on leaks, apparently from Portuguese officials.
No one has been charged and Portugal's Justice Minister Alberto Costa said last month that the police investigation into the disappearance was nearing its conclusion.