A system and method for operating a ventilator to compensate for external gas flow reaching a patient from an external device, such as a nebulizer. A control unit of the ventilator monitors the gas flow rate from the ventilator and compares the gas flow rate from the ventilator to an expired gas flow rate from the patient. The difference between the inspired flow rate and the expired flow rate is due to the external device. The control unit modifies the operation of the ventilator to compensate for the external gas flow rate such that the flow of gas reaching the patient is maintained at a desired level.
