Little has been reported on the safety and efficacy of pituitary biopsy in the pediatric population for suspected germinoma. An updated review is needed. Patients who underwent biopsy (endoscopic endonasal vs. open craniotomy) for isolated pituitary stalk thickening were identified. Age, pre- and post-operative endocrine status, surgical approach, length of surgery, estimated blood loss, surgical morbidity, length of ICU stay, total length of stay, and pathology reports were reviewed. Nine patients met inclusion criteria. Germinoma diagnosis was rendered in 7 of 9 patients; 1 patient required two biopsy attempts. Two-patients had histology consistent with inflammation and a subsequently self-limited disease course. Average operative time, blood loss, ICU stay and overall length of stay was just over 2 h, 28 mL, 1.6 days and 3.7 days respectively. There were no intraoperative complications and all patients were discharged home. One patient developed new diabetes insipidus post-operatively. Patients who underwent endoscopic biopsy had decreased operative times and shorter hospitalizations. Biopsy for isolated pituitary stalk thickening for suspected germinoma is generally safe with high diagnostic utility. Importantly, 22% of presumed germinomas on imaging yielded alternative diagnoses on biopsy, adding support for pathology-proven data to guide treatment in relevant cases.