In a major restructuring effort that sees core games boss Danny Bilson leave the company, industry veteran Rubin takes over as president with immediate effect, reports Eurogamer.
Announcing the appointment, THQ CEO Brian Farrell said: "Jason's proven track record in the industry speaks for itself, and he is one of the brightest minds in the business.
"We believe he can be a game changer and can contribute immensely to executing on our strategy of delivering quality connected core game experiences."
Rubin co-founded Naughty Dog with Andy Gavin in 1984 and had a hand in creating franchises such as Crash Bandicoot and Jak & Daxter.
He left Naughty Dog to pursue other projects in 2004.
> 'Darksiders 2, Metro: Last Light' lead THQ's future plans
> 'Company of Heroes 2' first-look preview: Moving to the Eastern Front
2012 has been a difficult year for THQ. In March, the company cut upwards of 120 jobs from two different studios, following the repackaging of its planned Warhammer MMO as a single-player game with multiplayer elements.
The company had previously revealed a net loss of $55.9 million (£35.4 million) for the three-month quarter ending December 31, 2011.
This prompted CEO Brian Farrell to announce plans to halve his current salary.
THQ will now shift its focus to titles such as WWE 13, Company of Heroes 2, and the recently delayed South Park: The Game.
Watch a trailer for upcoming THQ-published release WWE 13 below: