Developing guidelines for the role of the physiotherapist in neonatal and pediatric intensive care units is essential because these professionals are responsible for the rehabilitation of critically ill patients. Rehabilitation includes the evaluation and prevention of functional kinetic alterations, application of treatment interventions (respiratory and/or motor physiotherapy), control and application of medical gases, care of mechanical ventilation, weaning and extubation, tracheal gas insufflation, inflation/deflation of the endotracheal cuff protocol, and surfactant application, aiming to allow patients to have a full recovery and return to their functional activities. In this article, we present guidelines that are intended to guide the physiotherapist in some of the prevention/ treatment interventions in respiratory therapy (airway clearance, lung expansion, position in bed, airway suction, drug inhalation, and cough assist), which help in the rehabilitation process of newborns and children in intensive care units during mechanical ventilation and up to 12 hours following extubation.