Whelan set up the renewable energy developer along with chief executive Eddie O'Connor in 2008. He leaves to pursue other interests.
He said, "I am very proud to have played a role in setting up such a pioneering company... however there are other things I want to do now."
Mainstream's head of corporate finance Paul Corrigan will take over Whelan's responsibilities.
Before Mainstream, Whelan worked as corporate finance manager at O'Connor's previous venture Airtricity before it was sold to SSE in 2008.
O'Connor paid tribute to his business partner, "Fintan was very instrumental in the company's growth and success and I wish him all the very best in his future endeavours."