The classification of endometrial stromal sarcoma (ESS) has been refined and aided by the discovery of various recurrent gene translocations. Low‐grade ESS (LG‐ESS) is most commonly characterized by JAZF1‐SUZ12 fusions followed by rearrangements involving PHD finger protein‐1 (PHF1) and multiple fusion partners, including JAZF1, EPC1, EPC2, and MEAF6. In the present study, integrating anchored polymerase chain reaction and paired‐end next‐generation ribonucleic acid sequencing, we identified the presence of a novel malignant brain tumor domain‐containing 1 (MBTD1)‐PHF1 gene fusion in a case of LG‐ESS. MBTD1 belongs to the Polycomb gene group, and its fusion with PHF1 is predicted to mediate tumorigenesis through aberrant transcriptional repression. Histology and immunohistochemical studies demonstrated conventional morphology for LG‐ESS and clinical follow‐up showed no progression of disease after 6 months. These findings help expand the current knowledge on the spectrum of gene rearrangements in the diagnosis of ESS.