The notoriously mysterious Haymon has guided Mayweather's career for years and is widely regarded as one of the most influential men in boxing.
The Bolton boxer said: "I am very happy to have signed with Al Haymon, who has not only shown that he is a very astute businessman, but is extremely knowledgeable of the fight game and always has his fighters' best interests at heart."
Khan, the former Olympic silver medalist, had hoped to make his welterweight debut with a dream shot at pound-for-pound king Mayweather next month.
However, after spending weeks dangling a carrot in Khan's direction, the American instead opted to face the in-form Argentine Marcos Maidana.
Khan instead faces former Ricky Hatton opponent Luis Collazo on Mayweather's Las Vegas undercard, but still hopes to meet 'Pretty Boy' in the future.
Those ambitions have been further boosted by his deal with Haymon, who also looks after former Khan conqueror Danny Garcia as well as Adrien Broner and others.
"I'm looking forward to building a long and successful relationship during this exciting stage of my career," Khan added.
The former light-welterweight has been without a manager figure since parting company with family friend and long-time business manager Asif Vali last year.
Despite his notoriety, reputation and influence, Haymon maintains a phantom-like persona in boxing circles. Regularly name-checked by the likes of Mayweather, the former music executive has close links with American television paymasters and promoters, particularly Khan's own promoter, Golden Boy.