The 55-year-old was put forward by the Professional Game Board to replace Premier League chairman Sir Dave Richards in the role. The recommendation was endorsed by the FA Board and then approved by the FA Council.
Gill said: "I'm delighted to have been appointed vice-chairman of the Football Association. The health and success of the Football Association is vital to the future of the game in England and I hope to justify the board's faith in me by helping to shape discussions and actions to deliver that."
Gill, an FA board member for six years, will join Roger Burden, who represents the amateur game, as one of two FA vice-chairmen.
He is also the FA's nomination for the UEFA executive committee at the elections in May.