Background This study aimed to explore the 90% effective dose (ED90) of remimazolam in paediatric same‐day bidirectional endoscopy (BDE) and provide a more scientific dosage selection for the anaesthetic induction application of remimazolam in children. Methods The children were divided into a preschool (PS) group and a school‐age(S) group, the ED90 of remimazolam was determined using the biased‐coin up‐and‐down sequential test, the initial dose of remimazolam was 0.4 mg/kg in the PS group, 0.3 mg/kg in the S group, with a dose interval of 0.02 mg/kg. And remifentanil 5 μg/kg was combined as the analgesic drug. Results A total of 110 children were included in the study, 55 in each of the two groups. In the PS group, the dose range of remimazolam was 0.38–0.68 mg/kg, and the ED90 and ED50 were 0.67 mg/kg and 0.60 mg/kg using Centered Isotonic Regression (CIR); in the S group, the dose range of remimazolam was 0.30–0.48 mg/kg, the ED90 and ED50 was 0.45 mg/kg and 0.37 mg/kg using CIR. No serious adverse effects of remimazolam were seen in both groups. Conclusions In the induction of anaesthesia for same‐day BDE, combined with 0.5 μg/kg of remifentanil, the younger the age, the higher the dose of sedative medication required. The ED90 of remimazolam was 0.67 mg/kg [90% confidence interval (CI), 0.66–0.76] in preschool children and 0.45 mg/kg (90% CI, 0.42–0.59) in school children. Clinical trials NCT06121609, date of registration: Nov. 07, 2023.