Fort Bend County sheriff's deputies said they are getting conflicting stories, but their best guess is that the teen was shot in a shopping center parking lot off Highway 6 and Teal Bend Boulevard.
The teen claimed he was shot somewhere else, but a manager reported hearing two gunshots at the shopping center, deputies said.
At least one shell casing was found at the scene.
The 16-year-old was taken to the hospital and is expected to survive.
Deputies did not provide any further information about a possible suspect or motive in the shooting.