The present study analyzed the outcomes of patients with early-stage hypopharyngeal squamous cell carcinoma (HPSCC) treated with radical radiotherapy (RT) or concurrent chemoradiotherapy (CCRT). We retrospectively reviewed the clinical records of 33 patients with early-stage HPSCC who underwent RT or CCRT between January 1999 and December 2011. Of the 33 patients who were treated, 12 had Stage I and 21 had Stage II disease. Patients with Stage I were typically treated with RT, while patients with Stage II were treated with CCRT (concurrent chemotherapy: 5FU, cisplatin or TS-1). The median follow-up period was 81 months, ranging from 15 to 155 months. The 5-year overall survival rates, cause specific survival rates, locoregional control rates, and progression-free survival rates were 58, 75, 56, and 49 %, respectively. Of the 33 patients, 51 % experienced second primary malignancies. Esophageal carcinoma occurred in several cases, and was diagnosed either during screening after treatment for the second primary malignancy or simultaneously with the second primary malignancy. Advanced-stage second malignancies significantly influenced the survival of the patients and the control rate for HPSCC. Treatment emphasizing the quality of life after treatment is needed, if a poor prognosis is expected because of advanced-stage second primary malignancy.