Ethiopia, which alongside neighbor Kenya has for many years dominated distance running, had its credibility questioned earlier this year when six of its athletes came under investigation for doping.
It subsequently announced that it would carry out tests on up to 200 athletes.
The east African nation is also struggling with a slump in form and won a single gold medal at the Olympics in Rio de Janeiro in August, its poorest haul since 1992.
Amid discontent over mismanagement, Ethiopia’s track body held a closed-door assembly and elected Gebrselassie as its chief late on Saturday.
“I feel so honored to be elected president of the Ethiopian Athletics Federation! Will work on a great future for Ethiopian athletics,” Gebrselassie said on his Twitter account.
In August, Gebrselassie said the whole athletics set-up “needed a revamp”.
Gebrselassie, considered one of the sport’s greatest distance athletes, gave up competitive running in March last year.
Nearly unbeatable on the track in his prime, he won the first of eight indoor and outdoor world championship gold medals at Stuttgart in 1993 and went on to hold world records from the 5,000 meters to the marathon.
He won Olympic gold in the 10,000 meters in 1996 in Atlanta and 2000 in Sydney.
Gebrselassie has since focused on business interests and is involved in real estate projects, owns four hotels, a coffee plantation and is an automobile distributor.