Kroger's New Bern Avenue and Martin Luther King, Jr. Boulevard stores have been in operation since 1993 and 2002 respectively.
Fourteen stores will remain open in Wake and Durham Counties.
A statement said the company will try to secure employment for workers in the store that will stay open.
"As a grocer committed to providing our local shoppers with quality food and healthy options while keeping costs low, we are truly saddened to see the doors close to locations that have been present in the community for more than a decade," said Carl York, advertising & public relations manager for Kroger's mid-Atlantic marketing region. "We thank all the customers who are loyal shoppers at these stores and encourage them to visit our other locations in the Triangle. Kroger will continue its commitment to invest in our local community however we can."
The company said both locations being closed have been unprofitable.