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Plain English summary Intracranial germ cell tumours (iGCT) are relatively rare brain tumours that predominantly occur in paediatric patients. Since the survival rate of patients with iGCT has been improving and the burden of long-term morbidity is substantial, promoting the health-related quality of life (HRQoL) and reducing depression and anxiety among its survivors is of critical concern. Although many studies have been published on factors related to the HRQoL of iGCT survivors, little is known about their long-term emotional function. This study demonstrated the clinical factors that affect depression, anxiety, and the HRQoL and the associations between the HRQoL and depression/anxiety in 200 paediatric iGCT patients. We found that patients with recurrent tumours had a worse HRQoL. Tumour locations also played a critical role in that tumour involving the basal ganglia were associated with worse outcomes. A large proportion of paediatric iGCT survivors had depression or anxiety in all the groups. Depression/anxiety scores were highly correlated with the HRQoL emotional functioning scores. In addition, we found that the PedsQL parent proxy report is appropriate in most cases when it is not possible to obtain child self-reports. These findings provide evidence to support the optimization of treatment strategies for iGCTs, such as the provision of psychological interventions.