A man was also shot, and both victims were transported to an area hospital, where the man was pronounced dead.
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The 911 call was placed around 10:30 a.m. inside the El Campasino Deli on Caleb's Place in Central Islip after the gunfire rang out.
Officials believe the man was targeted but that the woman, an employee at the deli, was innocent.
Those who live in the area say everyone knew the clerk who was wounded.
"She's a nice girl," neighbor Kenneth Evans said. "It's terrible what happened to her."
Police believe the shooting is gang-related, but the investigation is ongoing.
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Anyone with information regarding the incident is encouraged to call Crime Stoppers at 1-800-220-TIPS.