With the application of next-generation sequencing (NGS) in soft tissue tumors, gene rearrangement is becoming known to pathologists as a molecular hallmark of spindle cell tumors, and other spindle cell tumors with related kinases are being reported. However, cases of rearranged spindle cell tumors not associated with rearrangements are rarely reported. Here, we describe a case of rearranged spindle cell tumor in a 3-year-old girl who presented with swelling and pain in the arm. Histologically, the tumor consisted of a fascicular arrangement of monomorphic spindle cells infiltrating and growing in adipose and muscle tissue with visible mitotic activity. Immunohistochemistry showed spindle cells negative for CD34, positive for S100 protein, and focal staining for Pan-TRK. fusion was identified by NGS. Fluorescence in situ hybridization (FISH) analysis confirmed the gene rearrangement but did not detect the gene rearrangement. In conclusion, we describe a rare case of CD34-negative, S100-positive spindle cell tumor with fusion.