The 31-year-old, who has not fought since his knockout defeat to Saul 'Canelo' Alvarez in May 2016, has signed a three-bout deal with Hearn's company.
The former two-weight world champion, who will take on his first opponent on April 21 at The Echo Arena in Liverpool, has previously been critical of Hearn's conduct.
Last year, Khan admitted his dislike for the 38-year-old while discussing a potential all-British fight against Matchroom's Kell Brook.
"The only way I would take that Brook fight is if he left Eddie Hearn. I just don't like Eddie Hearn," the Bolton-born boxer told reporters. "He's very disrespectful and he's never come clear with me."
Now, though, Khan is aiming to get his boxing career back on track with Hearn by his side.
"I'm thrilled to be teaming up with Matchroom," Khan said in a statement. "I've been out of the ring for too long, and I'm desperate to make up for lost time, starting in April.
"This decision is not one I've taken lightly, as I'm at a hugely important time in my career, but having spoken to Eddie at length, it was clear he and I were on the same page in terms of what I want to be doing and what I still want to achieve.
"I'm determined to win another World Championship and I'm confident I've got the right team behind me to help me do so. British boxing is in such a good place and I genuinely can't wait to get back in that ring with the incredible home support behind me."
A photo I never thought I would see! I'm delighted to announce the signing of @amirkingkhan to @MatchroomBoxing and @SkySportsBoxing returns to the ring April 21 @EchoArena 👌🏼 pic.twitter.com/iDdTKMYBtH— Eddie Hearn (@EddieHearn) January 10, 2018
In the last 18 months, Khan has had an operation on his right hand and his proposed fight with Manny Pacquiao fell through.
The Brit also recently appeared on ITV reality show I'm A Celebrity...Get Me Out Of Here.