Magnetic resonance imaging (MRI) and the computed tomography (CT) are the gold-standard imaging techniques in the management of atypical teratoid rhabdoid tumors (ATRT). One feature of this tumor entity is disturbance of cerebrospinal fluid (CSF) flow by either metastases or due to rapid tumor growth causing ventricular obstruction. In this situation, nuclear medicinal techniques for the depiction of cerebrospinal fluid (CSF) can be useful for detecting and evaluating CSF shunt passage as well as sites of possible obstruction, especially for further planning of intrathecal treatment. In the following case report, a 6-month-old male infant with a history of an ATRT and a complex CSF circulation situation after multiple interventions with a need of intrathecal therapy will be presented underlying the importance of CSF scintigraphy as an imaging tool for the functional representation of CSF flow for further treatment decisions and management of the patient.