The American, who takes up the role in the wake of Ron Dennis' controversial departure last week, will join the company on an unspecified date next month.
McLaren said that Brown's appointment would be "a significant part of a restructuring program that will align the Group's commercial and strategic operations relating to achieving success in Formula One."
Both Brown and chief operating officer Jonathan Neale will lead the company, reporting directly to McLaren Technology Group's Executive Committee, while the search for a new CEO continues. Following that, Brown will focus on a racing orientated role.
Brown was previously linked with a role with F1's new owners Liberty Media.
"I'm immensely proud to be joining McLaren Technology Group," said Brown. "Having worked closely with McLaren for many years, I've been struck by the talent and ambition of the entire workforce, and I very much look forward to complementing the business's many existing strengths, and building on them to drive future success in everything we do."
Zak Brown is no stranger to McLaren. The former-CEO of Just Marketing International is a co-owner of Anglo-American racing team United Autosports which campaigns McLaren GT3 cars in various championships.
He also famously persuaded Ron Dennis to let him become one of the very few to purchase a McLaren Formula One car when he bought Mika Hakkinen's 2001 British Grand Prix winning McLaren MP4-16A in 2014.
Dennis, meanwhile, will remain involved with McLaren as a 25% stakeholder.
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