The 46-year-old, who is also a member of the International Olympic Committee, was controversially beaten by Reverien Ndikuriyo, a Senator in Burundi's Upper House in Parliament.

He polled 56 votes to Nsekera's 31, ending her nine-year reign.

Until August, when Isha Johansen was elected President of the Sierra Leone Football Association, she had been the only woman to lead a national football federation.

FIFA and the Confederation of African Football (CAF) representatives who observed the election said today it had been free and fair.

Ndikuriyo, a former rebel fighter, is head of the "Black Eagle", a Second Division team in Burundi's Southeastern Makamba Province.

The position of Lydia Nsekera, seen here with Sepp Blatter, on the FIFA Executive Committee will not be affected by her election defeat @FIFA via Getty Images

Elections, delayed since February, were stalled by fighting between the rival contenders for the post, with Ndikuriyo backed by the ruling party CNDD-FDD.

Nsekera, who had been been co-opted to FIFA's Executive Committee in 2012 before being voted in by the world governing bodies member countries at the Congress in Budapest in May, will continue in the role despite losing her national power base.

Her position on the IOC is also not affected by her defeat and she will continue to serve on the Coordination Commission for Tokyo 2020, which it was announced last month she would serve on.

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