This questionnaire-based study reported health related quality of life (HRQoL) of 119 patients with head and neck cancer at 0, 6, 12, 24 months after proton therapy. Compared with the patient’s baseline conditions, patients reported worse in function of swallowing, sense, speech, and social eating and showed a series of treatment-related symptoms (i.e., dry mouth, sticky saliva, cough and feeling ill) at the end of treatment. At the six months follow-up, most of the functions had been restored, except pain, problems with teeth, dry mouth and sticky saliva. The result of the one-year follow-up indicated that pain had improved, however, the problem with teeth, dry mouth and sticky saliva symptoms had not disappeared one year after the end of treatment. The prevalence of dermatitis, xerostomia, mucositis, and dysphagia peaked at the end of PT and slowly reduced in the following year. However, only dermatitis, mucositis and dysphagia dropped back to baseline levels, while xerostomia remained present at higher levels compared to baseline during the entire observation period.