Involuntary respiration is controlled by the respiratory centers of the upper brainstem. The cerebral cortex of the brain controls voluntary respiration.

Two main parts of the brain control involuntary ventilation; the medulla oblongata and the pons. The brainstem contains central chemoreceptors that detect pH levels in the blood and send signals to the respiratory centers of the brain to adjust the ventilation rate to change acidity by increasing or decreasing the removal of carbon dioxide by exhalation. This removal of carbon dioxide causes the removal of hydrogen ions from the blood by the bicarbonate buffer system.

The medulla oblongata is the primary respiratory control center. Its principal function is to send signals to the muscles that control respiration that causes breathing to occur. There are two regions in the medulla that control breathing: the ventral respiratory group stimulates expiratory movements, and the dorsal respiratory group stimulates inspiratory movements. The medulla also controls the reflexes for nonrespiratory air movements, such as coughing and sneezing reflexes, as well as other reflexes, like swallowing and vomiting.

The pons is the other respiratory center and is located underneath the medulla. Its primary function is to control the rate or speed of involuntary ventilation. It has two main functional regions that perform this role: The apneustic center sends signals for inspiration for long and deep breaths. It controls the intensity of breathing and is inhibited by the stretch receptors of the pulmonary muscles at a maximum depth of inspiration, or by signals from the pnuemotaxic center. It increases tidal volume. The pnuemotaxic center sends signals to inhibit inspiration that allows it to control the respiratory rate finely. Its signals limit the activity of the phrenic nerve and inhibit the signals of the apneustic center. It decreases tidal volume. These two centres work antagonistically against each other to control the respiratory rate.

The primary motor cortex is the neural center for voluntary respiratory control. More broadly, the motor cortex is responsible for initiating any voluntary muscular movement. Different parts of the cerebral cortex control various forms of voluntary respiration. Initiation of the voluntary contraction and relaxation of the internal and external intercostal muscles takes place in the superior portion of the primary motor cortex.

There are several nerves responsible for the muscular functions involved in respiration. There are three types of important respiratory nerves: The phrenic nerves stimulate the activity of the diaphragm, the vagus nerve innervates the diaphragm as well as movements in the larynx and pharynx and the posterior thoracic nerves which stimulate the intercostal muscles located around the pleura.