16-year-old Cassidy Geffert was found safely in Brockport within an hour of the alert going out.
Geffert is said to have been found in an Econo Lodge motel where she was taken into custody.
Police say the Felony Grand Larceny charge stems from a gun being taken from the home in which Geffert was reportedly missing from in the Rochester suburb of Greece
Geffert entered a not guilty plea in court Monday evening.
She was released under her mother's supervision and must wear an electronic home monitoring bracelet, undergo a mental health evaluation, and all weapons must be removed from her home.