The aim of this study was to investigate the prevalence, severity, and pattern of evolution of swallowing impairments encountered in head and neck cancer (HNC) patients before and after chemoradiation (CRT) with videofluoroscopy of swallowing study (VFSS), using the modified barium swallow impairment profile (MBSImP) protocol and scoring system, and to determine the appropriate time points in which these patients should undergo VFSS post-CRT. A prospective cohort of 69 patients with locally advanced HNC underwent VFSS with the MBSImP protocol at 5 evaluation points: pre-CRT, and 1, 3, 6, and 12 months post-CRT. VFSS was scored with MBSImP, penetration-aspiration scale (PAS), and swallowing performance status (SPS) scale. Statistical analysis was performed only for the 12-month disease-free subset of patients. MBSImP, PAS, and SPS scale scores reached their peak at 3 months post-CRT and improved at 6-12 months, but without returning at pre-treatment levels. Base of tongue retraction, initiation of pharyngeal swallow, epiglottic movement, laryngeal vestibule closure, and laryngeal elevation were the most frequently observed impaired MBSImP components. Epiglottic movement significantly improved (p = 0.009) and laryngeal vestibule closure significantly deteriorated (p = 0.042) over time (Friedman test). Severe swallowing deficits and high aspiration rates are observed in HNC patients pre-CRT, which further deteriorate post-CRT, peak at 3 months, and despite slight improvement, persist over time. We suggest that these patients, regardless of the presence of subjective dysphagia, should undergo VFSS both before and 3 months post-CRT, and also if possible, 1 month post-CRT, in order to facilitate implementation of early swallowing rehabilitation.