Craniospinal irradiation using helical tomotherapy (HT-CSI) has advantages in aspects of homogeneous dose distribution. Physicians, however, still have concerns of pulmonary toxicity due to HT-CSI’s relatively large, low-dose irradiated volume from continuous and 360° rotation delivery. In this study, we investigated the pulmonary toxicity of HT-CSI. We retrospectively reviewed 105 patients who received HT-CSI between January 2014 and December 2019. Grade 2 + pulmonary toxicities were evaluated. Intensive systemic treatment was defined as systemic treatment administration before, during, and after HT-CSI. VX Gy was defined as % volume receiving ≥ X Gy. Thirteen patients (12.4%) presented with grade 2 + pulmonary toxicities after HT-CSI. Of these patients, only one experienced grade 2 radiation pneumonitis combined with pembrolizumab-induced pneumonitis. Conversely, pneumonia was observed in 12 patients. Intensive systemic treatment (p = 0.004), immunosuppressive drugs (p = 0.031), and bilateral lung V5 Gy ≥ 65% (p = 0.031) were identified as independent risk factors for pneumonia. The risk factor for pneumonia in pediatric patients were immunosuppressive drugs (p = 0.035) and bilateral lung V5 Gy ≥ 65% (p = 0.047). HT-CSI can be a safe treatment modality with tolerable pulmonary toxicities. Intensive systemic treatment, immunosuppressive drugs, and bilateral lung V5 Gy ≥ 65% were significantly associated with pneumonia. In these patients, close follow-up should be considered for proper management of pneumonia.