The money is to be used as a part of a legal defense fund for Kate and Gerry McCann, a Virgin spokeswoman said. The tycoon also urged other wealthy Britons to contribute.
The couple's daughter, Madeleine McCann, was three years old when she went missing during the family's vacation. She has been the subject of a Europe-wide search since her disappearance was reported.
After Portuguese police recently named Mrs McCann as a formal suspect in the case, the couple, both 39-year-old doctors, discussed selling their house to cover legal costs. They had refused to touch the money, over a million pounds ($2 million), already contributed to the Find Madeleine fund by members of the British public.
"In the midst of all of this speculation and rumor, we must remember there is a family in pain and a little four-year-old girl is still missing," Branson said in a statement. "We must not lose sight of this fact. It is the only solid fact we know. The search for Madeleine must not let up for one moment."
Portugal's public prosecutor has passed the case against the McCanns to a criminal judge who will decide whether there are grounds for a trial.
The couple deny any involvement in their daughter's disappearance.