The company had about 105,000 full and part-time employees previous year.
Most of the J.C. Penney stores on the closing list are in smaller communities.
The retail chain will close only two stores in Florida.
Nine stores will close in Texas, the most of any state.
Liquidation sales at the 138 stores will start next month, and most of the stores will be shut by mid-June, the company said.
The company said about 5,000 positions nationwide will be affected by the closures.
In addition to J.C. Penney, RadioShack, Hhgregg, Macy's, BCBG Maxazria and American Apparel have all announced closures in recent weeks.
Penney will close 4 stores in Iowa - in Decorah, Fort Dodge, Oskaloosa, and Ottumwa. The company filed a Worker Adjustment and Retraining Notification notice with the state Wednesday that it will lay off 119 employees there between May 19 and October 27.