Background: Phyllodes tumors (PTs) are a type of rare biphasic breast tumors that account for less than 1% of all breast tumors. Although malignant PT with heterologous sarcomatous differentiation is already a rare occurrence, it can further present with various types of differentiation, such as rhabdomyosarcomatous differentiation. Case Report: In this report, we describe the case of a 42-year-old woman who presented with a malignant PT with rhabdomyosarcomatous differentiation, an even rarer form of this tumor. To the best of our knowledge, only four confirmed cases of this type of PT have been documented in the literature. Conclusion: Due to its rarity, the diagnosis of malignant PT with rhabdomyosarcomatous differentiation can be challenging, and prompt recognition is essential for optimal patient management. Clinicians should keep this rare entity in mind when encountering patients with biphasic breast tumors and consider thorough pathological evaluation for accurate diagnosis and timely treatment.