Introduction The Cirq robotic alignment system (Brainlab, Munich, Germany) is a manually adjustable electronic arm with a robotic alignment module on its distal end, enabling the neurosurgeon to automatically and accurately align surgical instruments to a preoperatively planned trajectory. In this study, we share our first experiences and results using Cirq for intracranial tumor biopsy in children. Methods From May 2021 until October 2022, all consecutive patients that underwent a brain tumor biopsy using Cirq were included and compared to a historical cohort of patients biopsied with the non-robotic system Varioguide (Brainlab, Munich, Germany). Patient-related data, tumor-related data, and surgery-related data were collected. Registration accuracy was calculated for different patient-to-image registration methods. Pre- and postoperative images were fused, and entry error, target error, and angulation error were calculated. Results Thirty-seven patients, aged 1–19 years, were included (14 with Cirq and 23 with Varioguide). An integrated histopathological and molecular diagnosis was acquired in all cases. Patient-to-image registration was significantly more accurate when based on bone screw fiducials combined with intraoperative CT, as compared to surface matching or skin fiducials. The target error (Euclidian distance) was 5.3 mm for Cirq as compared to 8.3 mm for Varioguide, but this was not statistically significant. Entry error and angulation error were also not significantly different between both groups. Conclusion Intracranial biopsy with the Cirq robotic system is feasible and safe, and its accuracy does not differ from the Varioguide system.