The Pharmacy Section of Ciudad Medical Zamboanga is divided into In-Patient Pharmacy and Out-Patient Pharmacy, which deals with storage, compounding, packaging, dispensing and distribution of drugs.

The In-patient Pharmacy operates 24 hours daily, practicing Unit Dose Distribution System  (UDDS) wherein dispensing is organized and controlled, and prescribed drugs are contained in single unit packages that are delivered during the morning for a 24-hour period of medication.

The Out-Patient Pharmacy caters to the Medical Arts and walk-in patients, and opens from Monday to Saturday, 8am to 5pm only.