Thomson joins the league from Glasgow Rangers where he is currently head of commercial media, having previously held the position of commercial director at the Scottish Premier League.
Prior to working in football he held a number of senior sales and marketing positions at United Distillers.
Football League chairman Lord Mawhinney said Thomson's arrival would "further boost the upward momentum the league is enjoying commercially".
He added: “In recent seasons the league has established a healthy portfolio of commercial partners that includes Coca-Cola, Carling, LDV Vans, BT, Thomas Cook and Wickes. All have recognised the benefits the league can deliver through its clubs’ unique standing in their local communities.
Thomson takes on the role from January next year.
