Current chief executive Don Mattrick, who joined the company in 2013, will leave, effective immediately.
"I am returning to the company that I love in order to accelerate innovation," Mr Pincus said in a statement.
He will receive a salary of $1.
Mr Mattrick said he will return to his native Canada, adding: "I believe the timing is now right for me to leave as CEO [chief executive officer] and let Mark lead the company into its next chapter given his passion for the founding vision and his ability to couple our mobile progress with Zynga's unique strengths."
Although Zynga - known primarily for its once-popular Facebook games like Farmville and Words with Friends - has stabilised under Mr Mattrick, the company has continued to struggle.
In its most recent earnings release, Zynga said it lost $225.9m (Â£152m) in 2014, compared to $37m a year earlier.
However, it said its mobile audience continued to grow - showing that it no longer relied on Facebook to generate a majority of its traffic.
Shares in the company were up more than 3% in trading after US markets had closed.
Troubled game maker Zynga has announced that founder Mark Pincus will return to lead the company, as it struggles to repeat the success of hits like Farmville.