A method and apparatus for operating a ventilator to control the fraction of pressure inspired oxygen (FiO2) to a patient that includes: providing a ventilator controller that includes a software algorithm, a pulse oximeter and a FiO2 flow rate controller； measuring the pulse oximetry of the patient and computing an average pulse oximetry value over a time period； selecting a first, second and third pulse oximetry levels as set points for the ventilator controller； selecting an update time interval； decreasing the FiO2 flow rate by a first incremental amount when the average pulse oximetry value is greater than the first level； increasing the FiO2 flow rate by a second incremental amount when the average pulse oximetry value is less than the second level； increasing the FiO2 flow rate to the maximum and initiating an alarm condition when the average pulse oximetry value is less than the third level.
