The shooting happened inside the EZ-Mart on Walnut Avenue and Giddings Street on June 11.
Visalia police say the 16-year-old and a 15-year-old boy tried to rob the store.
During the robbery, officials say both suspects and the clerk shot at each other several times.
Officers found the clerk, 20-year-old Krish Singh, dead inside of the store.
The 16-year-old was found shot in the parking lot and later died in the hospital.
Investigators say the 15-year-old ran out of the store after the shooting.
He was arrested on Wednesday on a robbery warrant out of Porterville.
The teen has been booked for homicide and conspiracy at the Tulare County Juvenile Detention Facility.