Background The metabolic response of primary central nervous system lymphoma (PCNSL) patients has yet to be evaluated. This study aimed to assess the prognostic value of a novel scoring scale, the intracranial metabolic score (IMS), in PCNSL patients receiving end-of-therapy F-18-FDG PET/CT (EOT-PCT) and PET/MR (EOT-PMR). Methods The IMS was determined based on the metabolism of normal intracranial structures, including gray matter, white matter, and cerebrospinal fluid. The EOT-PCT cohort was evaluated using the IMS and commonly used Deauville score (DS). Another cohort of patients who underwent the EOT-PMR was used to validate the accuracy of the IMS. Results In total, 83 patients were included in the study (38 in PET/CT cohort, and 45 in PET/MR cohort). The area under the curve (AUC) values of the IMS for predicting PFS and OS were superior to those of the DS. When patients in the PET/CT cohort were stratified into five groups (respectively labeled IMS 1-5), three groups (IMS1-2, IMS 3-4, and IMS 5), or two groups (IMS1-3 and IMS4-5; IMS 1-4 and IMS 5), a higher IMS score was significantly correlated with poorer PFS and OS (p < 0.001). Similar results were observed for PFS in the PET/MR cohort (p < 0.001). The IMS and DS scale were found to be independent prognostic indicators for PFS and OS in the PET/CT cohort, and the IMS was identified as the sole independent prognostic indicator for PFS in the PET/MR cohort. Conclusion The IMS as a novel and effective prognostic tool for PCNSL patients, showing superior predictive value for patients' outcomes compared to the DS when assessed with EOT-PET scans.