The tycoon kicked off the day at the starting line of the half marathon before 10,000 people ran the 13-mile route around the Olympic Park in east London.
The fitness festival hosted multiple sporting activities, including a one-mile race for local primary school children.
Speaking at the event, Sir Branson said: “I think the obesity crisis in the UK is turning somewhat and I think it’s events like this that contribute to it getting better.
“I mean, I was watching the runners and slapping hands as they were running past me and I thought they must be going round and round – I just could believe there were so many people.
“It is just fantastic the amount of people who turn up for events like this.”
Sir Branson launched a confetti cannon off the top of a double-decker bus to commence the race, which took in the sites of Hackney Downs, Broadway Markey, Victoria Park and the London Stadium.
As he cheered on competitors, the businessman shared his views on ongoing Brexit negotiations, saying a “hard Brexit” would be a "disaster" for the UK.
He told the Press Association it was "important that people have a second chance" if "the facts change or once the facts are known", following negotiations to leave the EU.
"The people voted for the Government to come out of Europe based on £350 million more going into the NHS, and a whole lot of things they were promised,” he said.
"Let's see if these promises come true in a year or two years' time.
"And if those promises are not on the table and in fact the country is really suffering, and the costs are going to really cripple the country, then it's important, I think, there are MPs who can stand up and say something needs to be done about this - we can't just destroy a beautiful country."
The Virgin boss said that people had voted in last year's referendum without knowing the "truth", and said that "when everything has been negotiated, the House of Commons really should be given the facts and they should vote on whether it's a good idea or not".
"A hard Brexit would be, I think, a disaster for this country and therefore if they try to push that through, it's not what people were promised and it's important that people have a chance to have another think."