O’Rourke was Chairman of Football New South Wales (FNSW) for three years, from 2013 until March 2016.
He has also worked for PepsiCo Australia since 2006, and most recently served as Operations Director.
O'Rourke replaces Damien de Bohun, who served for four tumultuous years at the helm.
“Greg has the right skills and experience to drive the commercial performance of the A-League and its 10 member clubs,” said FFA CEO David Gallop.
“He also has decades of football administrative knowledge from service to the game at state and local level, including a successful tenure as chairman of Football NSW.
“Greg’s business acumen aligns with the FFA’s 2016-2019 Strategic Plan and the sharp focus on commercial performance in the strategy."
O’Rourke is the former President of Sutherland Shire Football Association, Australia’s largest suburban sports body.
“In many ways I’ve been working in football for years, but today I’m thrilled that the game will be my daily professional focus as well as a continuing personal passion,” said O’Rourke.
“The challenge is to lift the commercial performance of the A-League and its clubs with a strong emphasis on collaboration.
“The A-League is the shop window of Australian football, but the W-League, FFA Cup and the AFC Asian Champions League are crucial in the overall landscape.
"I know David Gallop and his team and I know they are a highly professional and experienced administration that I'm excited to work with."
Greg O’Rourke will officially commence as Head of the A-League in late August.