Sam Nyamweya was elected as the new Kenya FA boss on Saturday, ending seven years of wrangling within the administration of the game.
The former Kenya Football Federation secretary defeated his close rival Mohammed Hussein by a margin of 278 votes.
Nyamweya will head the new FA to be known as Football Kenya after outgoing chairman Mohamed Hatimy finished third.
Former Kenya international Sammy Sholei was elected the body's vice-chairman.
"I will commit this country to working closely with Fifa and Caf, by following their directives to make sure we take football forward," said Nyamweya in his acceptance speech.
Hussein criticised Fifa's Independent Electoral Board for not sticking to the guidelines and claimed the elections, which had been postponed twice this year, were neither free nor fair.
Since 2004, a private company, Football Kenya Limited (FKL), had been running the game in the country after earning recognition from Fifa.
A power wrangle ensued, with the government-recognized Kenya Football Federation (KFF) insisting it was also in charge.
Confusion then reigned in the organisation of Kenyan football for most of the intervening period, with the two bodies at one point running parallel leagues concurrently.
The squabling has adversely affected the growth of the sport in Kenya, with the national team now ranked at 135th globally by Fifa.