Both pharyngeal and esophageal phases of swallowing are under involuntary neuromuscular control.
The bolus will be formed by the tongue pressing the masticated food against the hard palate while the extrinsic lingual muscles push the bolus backwards. At the area of the palatoglossal folds (also called the Anterior Pillars of the Fauces or anterior tonsilar pillars), the pharyngeal phase of swallowing is initiated. In addition to the bolus contacting the anterior pillars, posterior tongue movement and stimulation of the pharyngeal mucosa and wall, are thought to stimulate the swallowing reflex. Stimulation of the internal branch of the superior laryngeal nerve can independently trigger the swallow reflex.

The sequential steps to pharyngeal phase of swallowing are:
Velum elevating to contact posterior pharyngeal wall and block upward movement of bolus into nasopharynx (called velopharyngeal port valving)
Elevation of the larynx and hyoid bone toward base of tongue, bringing a passive flipping over of the epiglottis to cover the glottis (opening to the larynx and trachea)
Contraction of pharyngeal constrictor muscles from superior to inferior direction
Opening (relaxation) of cricopharyngeal sphincter (also called the upper esophageal sphincter) to allow passage of bolus into esophagus
To keep food from coming out the nose when swallowing, the soft palate (also called the velum) will be elevated by the levator veli palatini muscles so that it comes into contact with the posterior wall of the pharynx. This area of the pharynx is specifically called the nasopharynx. The sides of the pharynx also contract and consequently move inward along with the posterior wall of the pharynx moving forward a little. This action creates Passavant’s Ridge.
One of the most important components of the swallowing process is the adduction (bringing together or “approximation”) of the true vocal folds (or cords) to protect the tracheal airway to the lungs. The cords have generally adducted before the larynx and hyoid have begun to elevate. The closure of the true vocal cords is the principal way the body protects against aspiration during a swallow. Once true vocal cord adduction has taken place, other adductions occur: false vocal fold adduction (the false cords sit just above the true cords), aryepiglottic folds, and finally, the flipping over (retroversion) of the epiglottis to cover the glottis (opening into the trachea).
While the action of the epiglottis protects the airway from laryngeal penetration and aspiration, it also acts to mechanically route the food bolus to the sides of the pharynx and towards the pyriform sinuses. These areas (the pyriform sinuses) as well as the hollows on each side of the superior facet of the epiglottis, called the valleculae (plural for vallecula), are places where residue of boluses may accumulate and create risk that particles of the residue may later move into the lungs.
There is a time period when no breathing necessarily takes place during the swallow, when the true vocal folds adduct. The swallow will tend to occur most often, in normal swallowing, during expiration. This will tend to lead to respiratory distress for a patient with poor lung function, as in disease states such as chronic obstructive pulmonary disease (COPD). Fatigue may build during a meal and the risk for aspiration climbs.
When the true vocal folds have approximated, pharyngeal peristalsis then takes place, evidenced by contraction of the superior, middle, and inferior pharyngeal constrictor muscles in order. Upon contraction of the first constrictor, laryngeal elevation is initiated. Laryngeal elevation takes place as the hyoid bone and tongue base more forward in synchrony with the contraction of the mylohyoid, geniohyoid, stylohyoid, and anterior digastrics muscles. The food bolus then moves into the cervical region of the esophagus.

The pharyngeal phase of swallowing lasts approximately 1 second.
Consistency of the boluses is important for therapeutic considerations because the more viscous the bolus, the greater the delay in pharyngeal transit as well as increasing the duration of pharyngeal peristaltic waves, and the longer the upper esophageal sphincter (UES) is open. On the other hand, the larger the volume of the bolus the earlier the tongue base moves, the longer the UES is open. The longer the UES is open, the greater its diameter. As the body ages, the pharyngeal transit time increases. The speed of the peristaltic wave in the pharynx is approximately 12 cm/second.
One swallowing researcher has described the swallowing process as a pressure-generation mechanism powered by a two-pump system. The oropharyngeal propulsion pump (OPP) and the hypopharyngeal suction pump (HSP) are the two components. The OPP is the pressure generated as the anterior two thirds of the tongue propels the food into the oropharynx accompanied by contraction of the pharyngeal constrictor muscles. The HSP is the negative pressure generated as the hyoid-laryngeal complex is elevated away from the posterior pharyngeal wall effectively drawing the food bolus towards the UES. Normal tongue movements are very important for normal swallowing because any condition that affects the anterior two thirds of the tongue will necessarily affect the OPP and that any problems affecting the tongue base will alter the HSP.
The UES provides a high pressure area separating the laryngopharynx and esophagus. It remains closed. Three muscles contribute to the structure of the UES: (1) the cricopharyngeus muscle, (2) the most inferior muscle fibers of the inferior constrictor muscle, and (3) the most superior portion of the longitudinal esophageal muscular fibers. These three muscles attach to the posterior lamina of the cricoid cartilage. Additionally, under the UES and lying along the posterior lamina of the cricoid cartilage, is the posterior cricoarytenoid muscle, the primary abductor of the vocal folds.
The cricopharyngeus has a continuous baseline muscle tone which relaxes during the swallow during elevation of the hyoid and larynx. The cricoid cartilage is pulled forward by the action of the hyoid bone and by contraction of the thyrohyoid muscle, snapping open the UES. T he UES then closes while the larynx is descending to its resting position. The UES has a sustained contraction before resuming its baseline muscle tone likely helping prevent immediate regurgitation as soon as the bolus enters the esophagus. The cricopharyngeus is thought to receive motor innervation from the vagus and glossopharyngeal nerves and from sympathetic branches with the cranial nerve ganglia. The vagus and glossopharyngeal nerves are also responsible for sensation in the cricopharyngeus.