The mission of the Booking Section is to provide a secure point of intake and discharge where individuals who have been remanded by a local court or persons arrested by Syracuse Police are processed into and discharged from the Justice Center. This section consists of two units: Public Services and Admissions & Discharge.

Public Services Unit: This unit consists of Community Service Officers and a Bail Cashier. The primary functions of the Community Service Officers include greeting the public in the lobby of the Justice Center, scheduling visits, and screening visitors entering the Justice Center. The Bail Cashier's duties include maintaining the financial accounts of inmates, and receiving, tracking and dispersing funds for the purpose of bailing inmates.

Admissions & Discharge Unit: This unit consists of Intake, Identification, Classification, Inmate Supervision, Admit/ Discharge, Property/Discharge, and Property Control deputies. Their primary functions are as follows: Intake: Initiates a booking computer record for individuals brought to the Justice Center, either under arrest or committed by a court in Onondaga County. Identification: Takes fingerprints and photo images of all inmates booked at the Justice Center, keeps and maintains records of the same. Classification: Does an assessment and Suicide Prevention Screening Form; makes medical and mental health referrals as needed. Initiates appropriate precautions to safeguard inmates, when necessary. Provides and obtains entrance information from each inmate as well as answering any questions they may have. Inmate Supervision: Introduces and explains the concept of direct supervision to all inmates. Observes inmates as they are being processed through booking and tracks their progress. Property: Responsible for securing, storing, and tracking property taken from inmates at the time of booking. Discharge: Conducts the process of discharging inmates out of the Justice Center, which includes returning all property and money belonging to them. Collects all property issued to the inmate during their incarceration.

Ultimately, all deputies assigned to the Booking Section are cross-trained in all of the responsibilities of processing inmates in and out of the Justice Center.