This study aims to assess the therapeutic effects of probiotic oral therapy in paediatric patients with anorexia nervosa (AN) and to investigate its impact on intestinal flora composition, brain–gut peptide levels and overall clinical outcomes. A retrospective study was conducted involving 100 children diagnosed with AN at Xingtang County People’s Hospital between January 2023 and June 2024. Patients were divided into two groups: a control group (n 50) receiving zinc gluconate oral solution alone and an observation group (n 50) receiving zinc gluconate plus probiotics. Outcome measures included intestinal flora analysis, brain–gut peptide levels (somatostatin (SS) and nitric oxide (NO)), clinical efficacy, serum trace element levels (Ca, Zn and Fe) and prognosis, including recurrence rates 6 months post-treatment. Baseline characteristics were similar between the two groups (P > 0·05). After treatment, the observation group showed significantly higher levels of Bifidobacterium and Lactobacillus and lower levels of Enterobacter compared with the control group (P < 0·05). Additionally, the observation group had lower levels of SS and NO (P < 0·05), indicating improved brain–gut communication. Clinical efficacy was significantly higher in the observation group (P < 0·05), with improved serum trace element levels (P < 0·05 for Ca, Zn and Fe). Furthermore, the recurrence rate 6 months post-treatment was significantly lower in the observation group compared with the control group (P < 0·05). Probiotic supplementation in children with AN effectively modulates intestinal flora, improves brain–gut peptide levels and enhances clinical outcomes.