The 43-year-old, who left a similar role at Leeds earlier this month after nine years, was already a member of the League's board.
Harvey will take up his new position on October 1, with chairman Greg Clarke moving from an executive to non-executive role.
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."
Harvey, who has also worked at Bradford and Scarborough, said: "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."