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.