Primary lymphomas of the female genital tract are rare, representing approximately 1% of extranodal lymphomas. The most common histological subtype is diffuse large B-cell lymphoma, followed by follicular lymphoma. Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) in the female genital tract is rare and usually discovered incidentally. While MALT lymphoma is often linked to infections or autoimmune diseases, its cause in the female genital tract is generally unknown. On the other hand, malakoplakia is a chronic inflammatory condition resulting from an impaired histiocytic response to common bacterial infections. In this report, we present an extremely rare case of concurrent primary MALT lymphoma and malakoplakia in the vagina of a 79-year-old woman who exhibited postmenopausal bleeding and a soft tissue mass. Tissue examination revealed malignant lymphoid cells obscured by abundant inflammatory cells interspersed with numerous blood vessels, mimicking granulation tissue. A significant diagnostic challenge lies initially in missing the concurrent presence of malignant lymphoma and malakoplakia. Therefore, we emphasize the importance of clinicopathological correlation to accurately diagnose these rare conditions.