Undifferentiated small round cell sarcoma of bone and soft tissue are rare, malignant neoplasms, often presenting diagnostic challenges due to its overlapping features with other conditions such as osteomyelitis and Brodie abscess. Accurate diagnosis requires a combination of imaging studies, histopathology, and genetic testing. Delayed or misdiagnosis can impact the prognosis and treatment outcomes. We present the case of a 34-year-old female who initially presented with persistent left upper thigh pain. Initial imaging raised suspicion of chronic osteomyelitis, with subsequent MRIs showing abnormal bone marrow edema and a lytic lesion in the left femoral diaphysis. Despite undergoing multiple biopsies, results remained inconclusive, with differential diagnoses including Brodie’s abscess. The patient experienced temporary improvement, but her symptoms recurred, prompting further investigations. A repeat MRI showed the progression of intramedullary lesions and the appearance of new focal lesions. A biopsy eventually confirmed the presence of a malignant round cell tumor, identified as Ewing sarcoma through immunohistochemical evaluation and detection of EWSR1 gene rearrangement on FISH analysis and further NGS confirming EWSR1-NFATC2 fusion, diagnostic of the rare entity — round cell sarcoma with EWSR1-NFATC2 fusion. This case highlights the diagnostic complexities of round cell sarcoma of bone, which can mimic other benign bone lesions. It underscores the importance of multidisciplinary evaluation, genetic testing, and timely oncological intervention to improve patient outcomes.