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Abstract Background Primary CNS lymphoma (PCNSL) is a rare, aggressive diffuse large B-cell lymphoma confined to the CNS, with poor outcomes. Virally associated PCNSL, including AIDS-related PCNSL (AR-PCNSL) and CNS post-transplant lymphoproliferative disorder (CNS-PTLD) accounts for ~10% of cases and is strongly linked to EBV infection and poor prognosis. In our prior Blood (Gandhi et al. 2021) study, targeted sequencing showed that EBV⁺ PCNSL lacks canonical MYD88, CD79B, and PIM1 mutations and retains intact HLA class I/II, suggesting distinct immunobiology. However, questions remain regarding the immune microenvironment, broad mutational landscape, and intratumoral heterogeneity. Here, we present the first large-scale comprehensive integrated analysis of virally associated PCNSL to define subtype-specific vulnerabilities and therapeutic implications. Methods FFPE brain biopsies from 72 PCNSL patients (40 EBV- de novo PCNSL, 32 EBV+ PCNSL including 18 AR-PCNSL and 14 CNS-PTLD) were analyzed. Immune gene expression was profiled using the NanoString PanCancer Immune Panel. Whole exome sequencing (WES) defined recurrent driver mutations, tumor mutational burden (TMB), and LymphGen classification (excluding A53 subtype). Single nuclei RNA sequencing (snRNA-seq) using the 10x Genomics Chromium Flex platform characterized cellular heterogeneity. Results WES demonstrated a marked reduction in canonical mutations (MYD88L265P, CD79B, PIM1, CARD11) in CNS-PTLD (0%) and AR-PCNSL (29%) vs. de novo PCNSL (87.5%; p<0.0001). AR-PCNSL had a distinct mutational signature when compared with CNS-PTLD and de novo PCNSL. NOTCH1/2 mutations were significantly enriched in AR-PCNSL (71%) vs. CNS-PTLD (9%) and de novo PCNSL (33%) (p<0.01). NLRC5 mutations were present in 64% of AR-PCNSL cases, higher than the 25% observed in de novo PCNSL and were absent in CNS-PTLD. TMB was significantly elevated in AR-PCNSL (mean 26.27 mutations/Mb) vs. de novo PCNSL (17.22) and CNS-PTLD (11.01; p=0.0018) underscoring pronounced genomic instability and suggesting HIV may exert a mutagenic influence beyond immunosuppression. EBV driven subtypes lacked MCD features and were more often classified as ST2 or unassigned. Despite NOTCH2 mutations, AR-PCNSL cases were not classified under the BN2 subtype, further highlighting limitations in current molecular classification systems to accurately stratify virally associated PCNSL. Immune transcriptomic profiling revealed further distinctions within EBV+ PCNSL. CNS-PTLD showed increased expression of genes related to antigen presentation (p<0.0001), cytotoxicity (p=0.0019), and T cell function (p<0.0001), suggesting retained immune responsiveness. AR-PCNSL exhibited significant suppression of HLA class I/II genes (p=0.0027 and p<0.0001 respectively), despite intact genomic loci, implicating post-transcriptional or epigenetic silencing. Immune cell composition revealed reduced macrophage infiltration and suppressed CD4 expression in AR-PCNSL. CNS-PTLD showed higher expression of checkpoint molecules LAG3, TIM3, and CTLA4, consistent with T cell exhaustion. snRNA-seq profiling of AR-PCNSL identified distinct malignant and non-malignant cell populations, including a reduced CD4⁺ compartment and altered microglial/macrophage populations and cell states compared to de novo PCNSL, corroborating bulk transcriptomic data, amongst other ongoing analysis. Conclusion This study represents the largest and most comprehensive immunogenomic investigation of virally associated PCNSL. AR-PCNSL and CNS-PTLD lack canonical PCNSL driver mutations and instead harbor distinct mutational signatures, including NOTCH pathway alterations in AR-PCNSL. These findings underscore divergent pathogenic mechanisms and support tailored therapies. AR-PCNSL is marked by high TMB, suppressed antigen presentation, and reduced CD4⁺ infiltration, indicating profound immune dysfunction. CNS-PTLD retains immune functionality but shows checkpoint upregulation and T cell exhaustion. Despite both being EBV-driven and CNS-restricted, they display distinct molecular and immunological programs, suggesting context specific EBV mechanisms. These findings challenge existing classification systems and support CNS-specific molecular frameworks to guide therapeutic interventions including BTK inhibition for NOTCH-mutated lymphoma. They lay the foundation for precision approaches in EBV⁺ PCNSL, including immune restoration, antigen-specific T cell therapy, and epigenetic modulation.