Randy Abbey was elected on Thursday at the GFA Headquarters together with Samuel Anim Addo and Mark Addo.
The three will represent the interest of Division One League clubs on the Council.
Randy Abbey, who is the Chief Executive Officer of Heart of Lions, polled 26 votes to beat eight others to emerge winner.
Mark Addo, who is the CEO for Nzema Kotoko, came a close second with 25 votes while Samuel Anim Addo, who owns Young Apostles FC, polled 19 votes to join Mr Abbey on the Council.
Among the candidates who missed out are Gideon Ofosu (17), Otuo Acheampong (14), Justice Boison (13), Alhaji Grunsah (9), Kweku Eyiah (7) and Eric Oppong (4).
Earlier, Madam Habiba Attah Forson, who founded Fabulous Ladies, was elected to represent the women’s Elite Clubs.
Linford Asamoah, who was last week elected as the Chairman of the Eastern Regional Football Association, was also elected to represent the RFAs on the Council.
A second position on the Council for RFAs has to be decided on Friday after both candidates polled a tie.
It will be between Central Regional FA Chairman Robert Duncan and Salifu Zida, who was elected last week as Upper East Regional FA Chairman.