The African Football Confederation (CAF) secretary-general, Hicham El Amrani, resigned on Sunday without giving an explanation.
The 37-year-old Moroccan revealed his decision in a letter to African national football associations.
His move is probably linked to the defeat of long-serving Cameroonian Issa Hayatou by Malagasy outsider Ahmad Ahmad in the CAF presidential election this month.
El Amrani was a Hayatou loyalist, constantly defending his boss, who ruled African football for 29 years, against public and media criticism.
He became secretary-general, initially on an interim basis, in 2010 when Egyptian Mustapha Fahmy moved to global football body FIFA.
Ahmad, who will serve a four-year term, is scheduled to meet CAF staff on Monday at the Cairo headquarters of the 60-year-old organisation.