The 43-year-old, who spent nine years as chief executive of Leeds before departing Elland Road earlier this month, will take up his new position on October 1 with League 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 was previously a member of the Football League board of directors, having been elected to the role by clubs in June 2011.
He started his career in football as club secretary of Scarborough in 1993 and spent 10 years as managing director of Bradford.
Harvey 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."