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Aims/Background Probiotics, including Bacillus licheniformis, have been shown to mitigate intestinal inflammation and mucositis by modulating gut microbiota and immune responses; however, their role in radiation-induced gastrointestinal (GI) injury remains unclear. This study aims to investigate the effects of Bacillus licheniformis supplementation on radiotherapy-induced GI dysfunction, inflammation, and survival rates in pediatric patients with medulloblastoma. Methods A total of 205 pediatric patients with medulloblastoma admitted to Jinhua Municipal Central Hospital between March 2015 and March 2020 were divided into an experimental group and a control group based on treatment protocols. All patients received craniospinal irradiation (CSI). Patients in the experimental group received an oral Bacillus licheniformis preparation (one capsule, three times daily) starting one day before CSI and continuing through the completion of radiotherapy, while the control group did not receive the probiotic. Post-radiotherapy adverse reactions were recorded. Serum levels of endothelin (ET), C-reactive protein (CRP), tumor necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6) were measured one day before the first radiotherapy session and one day after the final session. A five-year follow-up was conducted to assess patients' survival rates. Results Most of the pediatric medulloblastoma patients developed varying degrees of gastrointestinal symptoms after CSI, with fewer cases observed in the experimental group compared to the control group (all p < 0.05). Serum levels of ET, CRP, TNF-α, IL-1β, and IL-6 significantly increased post-radiotherapy in both groups, but the rise was markedly attenuated in the experimental group (all p < 0.001). However, no significant differences were found in 5-year progression-free survival (hazard ratio [HR] = 1.060, log rank p = 0.716) or overall survival (HR = 1.275, log rank p = 0.350) rates between the two groups. Conclusion Bacillus licheniformis preparation effectively alleviates CSI-induced gastrointestinal dysfunction and inflammation in pediatric patients with medulloblastoma, but does not significantly improve their survival rates.