The departure of Daniel Shugar follows a leave of absence that the executive took in March for nine to 12 months.
Shugar informed SunPower of "his decision to not return as an employee of SunPower or its affiliates," SunPower said in a filing with the U.S. Securities and Exchange Commission.
Shugar joined SunPower as head of its systems unit in 2007 when SunPower acquired PowerLight Corp, where the executive had worked since 1996.
The systems unit develops, engineers and manufactures large-scale solar power systems.
The solar power sector is looking for a stronger year in 2010 after a difficult 2009 with falling panel prices and tight credit for new renewable energy projects. The San Jose, California-based SunPower is also probing millions of dollars of accounting mistakes.