Hooper has agreed to a two-year deal with the Waratahs and will join the ACT Brumbies' arch-rivals at the end of the Super Rugby season.

The 20-year-old had been locked in contract negotiations before a game had been played this year, with Brumbies coach Jake White keen to secure the rising openside flanker.

It's a major blow to the Brumbies with Hooper leaving the club in career-best form.

However, they still have former Australian under-20s captain Colby Faingaa and Ita Vaea who will battle for the spot.

After spending the past three years away from his family, Hooper decided he needed to return to Sydney to continue his career.

''The lure to be back home and play rugby at this level would be a dream come true,'' Hooper said.

''It's all of things coming together, family and being back home near where I grew up.

''I grew up following the Waratahs and I've decided to go in that direction.

''I was very close [to remaining in Canberra], but the way things fell I thought this decision was the best one for myself.

''I've always thought it would be nice to go back [to Sydney] and it was only recently I made the decision because it was such a tough choice.''

Three years after breaking into the Brumbies' top squad, Hooper has evolved from a teenage talent to a potential Super Rugby star.

He has lifted his game to a new level this season and has earned the praise of Australia's World Cup winning captain John Eales and a host of past and current players.

He is in the midst of a breakout campaign as a dominant flanker.

But after agonising over his future since February, Hooper hoped his performances would get even better now he is no longer distracted by contract negotiations.

Hooper described the process of choosing the Waratahs as the ''toughest of my career'' and was relieved to have a deal finalised.

''It's good to have it behind me, it was a distraction for me,'' Hooper said.

''I was going into games not thinking solely about the game and that's distracting. I'm definitely a lot freer now in my thoughts.

''I came to Canberra out of school but I've never had a decision as hard as this.''

Hooper joined the Brumbies as a back-up to George Smith and earned his first starting cap in 2010 when Smith damaged nerves in his shoulder. But it has taken until this year for him to establish himself as a Super Rugby player.

White is adamant Hooper's defection will not count against him at the selection table.

And Hooper vowed to repay the faith by putting his body on the line for the Brumbies for the remainder of the year.

''I hope I can keep performing to be selected despite my decision to go next year,'' Hooper said.

''I'll give the Brumbies everything I have and will continue to do so until the end of the year.

''I chose the Brumbies over the Waratahs when I left school and the Brumbies were the shining light for me then, I wouldn't change anything.

''The No.7 for the Waratahs is a hotly contested spot and I think it's a good opportunity for me to go back and make that jersey my own.''

Brumbies forwards coach Laurie Fisher was disappointed to lose Hooper, but said his increased work rate this season had made him one of the competition's leading ball fetchers.

''Prior to this year he was making a lot of decisions not to go into contests at the breakdown and now he just goes in,'' Fisher said.

''He's putting his head in and competing and I think that change of mindset has been good for him.'' Chris Dutton