Burkitt lymphoma (BL) is a highly aggressive B-cell lymphoma with its occurrence and progression closely associated with Epstein-Barr virus (EBV) status. However, the molecular differences between EBV-positive and EBV-negative BL have not been comprehensively evaluated. Through targeted sequencing of a 475-gene panel in 27 BL cases, and RNA-seq and LncRNA-seq analyses of 25 cases, we found that EBV-negative tumors displayed a higher frequency of chromosomal amplifications, particularly at 7p12.2, 6q25.3 and 7q22.1. Two novel variants of KMT2D were identified in adult patients in the EBV-negative group. Furthermore, EBV-positive BL exhibited enriched FOXO1 mutations, in contrast to CCND3 hotspot variants in EBV-negative cases. Transcriptome profiling revealed 1,612 differentially expressed genes (DEGs), predominantly involved in the PI3K-AKT, Hippo, WNT, and mTOR pathways. LncRNA profiling identified three EBV-associated lncRNAs ((MSTRG.103766.1, MSTRG.33752.11, ENSTO0000400385.2) with potential prognostic relevance in BL. Immune deconvolution (CIBERSORT/xCELL) demonstrated elevated M1 macrophages infiltration in EBV-positive BL, which correlated with improved 24-month overall survival (68% vs. 41%, p = 0.02). SULT1C2P1 and KCNK5 emerged as M1-associated prognostic biomarkers. Our findings establish EBV as a key modulator of BL genomic instability and immune remodeling, leading us to hypothesize that EBV status defines distinct BL subtypes with unique therapeutic vulnerabilities, thereby enabling the future development of EBV-stratified precision therapies.