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Phyllodes tumors (PTs) are rare fibroepithelial neoplasms of the breast. PTs may pose significant diagnostic challenges, especially when they lack the classic leaf-like architecture and resemble cellular fibroadenomas. Accurate distinction between these entities is clinically important because of differences in management and recurrence risk. We report a 21-year-old woman who developed an early local recurrence of a fibroepithelial lesion initially diagnosed as a cellular complex fibroadenoma. The recurrence demonstrated stromal hypercellularity, multifocal infiltrative growth, and non-atypical smooth muscle differentiation without characteristic leaflike architecture, rendering morphological classification inconclusive. Next-generation sequencing demonstrated a pathogenic frameshift mutation in the BCOR gene. When integrated with the patient's clinical history and the lesion's morphology, these molecular findings supported a diagnosis of borderline PT. This report emphasizes the importance of integrating histopathological, clinical, and molecular data in the evaluation of fibroepithelial lesions with ambiguous morphology. Molecular alterations, such as BCOR mutations, may provide valuable diagnostic support, in particular in fibroadenoma-like PTs.