Nyantakyi, who is a member of FIFA's Organising Committee for the Olympics, will be working for the world governing body during the event in the United Kingdom.
He will be based in Coventry where he will supervise the organisation of football matches involving men and women during the three-week event.
Fred Crentsil will act as the leader of the GFA while Nyantakyi is away for three weeks.
Nyantakyi said his participation in the Olympic Games will greatly benefit Ghana.
"The Olympics is the biggest sporting event in the world and offers a lot of benefits," the GFA President said.
"It offers a lot of training and benefit to whoever has the opportunity to be a part of it.
"I believe that when I go the experience I gain will impact positively on my return on football in this country."
Crentsil was named as the stand-in leader of the GFA because he is the longest serving member of the Emergency Committee.
Meanwhile, Nyantakyi made some key announcements of a raft of proposed changes to the regulations of the GFA.
Below are some of the changes to be put before Congress in September:
*The phased implementation of the club licensing system.
*The proposal to use the single-judge system for the Disciplinary Committee.
*The reduction of the time for protests in respect of inter-club matches. Clubs must lodge protest no later than 24 hours from the end of the match. Previously it was 72 hours.
*The abolition of the review system in the legal processes of the GFA.
*The introduction of distinct home and away strips for clubs.
*The introduction of a unified calendar for all the leagues and competitions in the country.
*Protesting clubs won't benefit points-wise in certain protests.
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