Background Pilocytic astrocytoma is a slow-growing and benign tumor usually treated with craniotomy; however, the resection of deep-seated lesions remains challenging and often ends only with biopsy. Recently, an endoscope equipped with 5-aminolevulinic acid (5-ALA) photodynamic diagnosis was introduced. To improve the extent and safety of resecting these deep-seated tumors, we report a novel procedure of minimally invasive endoscopic resection of deep-seated pilocytic astrocytomas under the guidance of 5-ALA fluorescence undescribed until now. Case Description A 53-year-old male presented with a gradually progressing mild right hemiparesis. Imaging studies showed a solid tumor with degenerative cystic formation in the left basal ganglia. The tumor was removed endoscopically via right frontal small craniotomy. The tumor was positive for 5-ALA fluorescence and allowed better detection of the dissection margin of the solid tumor from the surrounding brain tissue. The histopathological diagnosis was pilocytic astrocytoma. No recurrence was observed on follow-up magnetic resonance imaging (MRI) 2 years after surgery, and the patient was fully independent after rehabilitation. Conclusion This minimally invasive technique, enhanced by intraoperative fluorescence, might be a safe and feasible alternative to open surgery in the removal of deeply located gliomas.