The 43-year-old, who had been Leeds’ chief executive for nine years, was previously managing director of Bradford City and club secretary at Scarborough.
Harvey added: “As someone who has served Football League clubs for most of my working life, it is a great privilege to be appointed to this role.
“I have the very highest regard for the people who run our football clubs and I look forward to working with them, as well as all those with a stake in our game, to deliver a vibrant and sustainable Football League.”
Harvey will take up his new position on October 1 with Greg Clarke moving from executive to non-executive chairman.
Clarke said: “Shaun is widely respected across the game for his deep understanding of the football industry. During my time as chairman, he has made an important contribution to the League Board.
“Having held senior positions at football clubs in all four divisions of English professional football, he is uniquely placed to understand the challenges faced by clubs of all sizes.”