Investigators say it all began with a burglar alarm at 5:15 a.m. at the West Trenton Pharmacy in the 600 block of Bear Tavern Road.
When officers arrived, they found the suspect still inside the store.
Police say the suspect fled and a Ewing officer fired one shot at the suspect.
That suspect, only described as a young man wearing a black ski mask, fled on foot.
Officers say he ran between several homes before getting away.
Police say two prescription bottles were recovered nearby, and the pharmacy is now checking inventory to see what was taken.