Epstein-Barr virus (EBV) is one of the most common viruses associated with multiple malignancies including hematopoietic, epithelial, and mesenchymal neoplasms. EBV is linked to B- and T-cell lymphomas, ranging from indolent to highly aggressive neoplasms. EBV-positive follicular lymphoma (FL) is not well characterized due to its low prevalence. In this report, we describe a case of EBV-positive FL and concurrent EBV-negative diffuse large B-cell lymphoma (DLBCL), and discuss their clonal relationship, and EBV status in the process of disease progression. Histology, immunohistochemistry, in situ hybridization, and next-generation sequencing studies were performed as previously described. The 58-year-old male presented with extensive axillary and subpectoral lymphadenopathy. The patient had a history of mixed connective tissue disease treated in the past with steroids and methotrexate, and at the time of current presentation with hydroxychloroquine. The excision of axillary lymph node showed coexistent EBV-positive FL (grade 3B) and EBV-negative DLBCL. There was no evidence of BCL2 gene rearrangement; however, both EBV-positive neoplastic follicles and diffuse component harbored MYC/IGH rearrangement. Next-generation sequencing suggested branching evolution with shared DDX3X mutation, a number of private mutations, and unique IGH usage in FL and DLBCL. The patient was treated with six cycles of R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone) with involved-field radiotherapy and remains in complete remission. To the best of our knowledge, this is the first report of BCL2 rearrangement negative, MYC/IGH-positive and EBV-positive FL, and concurrent EBV-negative DLBCL, which supports branched evolution model.