The contract, which will keep the 27-year-old at the club until at least 2015, has been awarded following Hopper's recent performances for the Aviva outfit.
Harlequins director of rugby Conor O'Shea told reporters: "We are thrilled about Matt's re-signing with the club. Matt is up there with the most competitive individuals any of our coaches have ever come across.
"His drive to be the best he can be is second to none and in just over a year since joining the club, he has represented England at Saxons level, played in some historic wins for this club and contributed greatly to us winning the Aviva Premiership.
"The important thing with Matt is that he is not satisfied with what he has achieved and wants more, we are looking forward to him realising his ambitions with Harlequins."
Meanwhile, Hopper added: "I'm very happy to have re-signed with Harlequins. In my short time at the club, I have been impressed with the level of dedication and passion shown by all members of the squad and I am thankful to have been a part of this.
"The style of rugby we are looking to play, matched by such a talented group of players, made my decision to stay very easy. I look forward to competing for a regular starting spot over coming seasons and hopefully being an integral part of what is already a successful team."
Hopper has previously played for the Cornish Pirates.