The present disclosure pertains to a system and a method for expiratory flow limitation (EFL) detection by controlling positive pressure (e.g., PEEP) applied during expiration for a subject. The technique is based on a temporary perturbation or adjustment of a pressure level of positive pressure during exhalation on selected breaths. The different response to such a perturbation that flow-limited breaths have compared to non-flow limited breaths is exploited to assess EFL in a subject. Adjustments of positive pressure applied to the patient are used in the disclosed algorithm to abolish EFL. The algorithm can be implemented in existing ventilators and other respiratory devices.