The American will replace Freddie Roach, who was let go by Khan following two consecutive defeats.
Hunter helped Andre Ward unify two world super-middleweight titles and was voted as Trainer of the Year by the Boxing Writers Association of America last year.
"I'm really pleased that Virgil Hunter is to become my new trainer," said Khan. "Everyone in boxing knows about his skills and the success he has enjoyed over the last few years.
"I'm looking forward to the start of my training camp and working on some new things with him.
"With Virgil in my corner, I know that I can get back to the very top of the light-welterweight division."
Hunter too is pleased with the newly-formed alliance.
"Amir is an extremely talented fighter and I'm very happy to become his new trainer," he said. "I've seen a lot of him and he has many attributes such as his speed and heart.
"There are certain small aspects of his game that I'm intending to work on in order to help him fulfil his enormous potential."
Hunter will prepare Khan for his upcoming fight against Carlos Molina in the United States, with the date still to be decided.