The company is one of the most high-profile retailers to file for bankruptcy protection after being hit hard by the coronavirus and said it expects store closing sales to last around three months.
Seven other California locations will also close, including stores in Delano, Tracy and Turlock.
The JC Penney at Fresno's Fashion Fair will remain open for now.
JCPenney filed for Chapter 11 last month.
Economists say the pandemic's hit on sales was the final blow to a 118-year-old company struggling to overcome a mountain of debt.