Selective tyrosine kinase inhibitor (TKI) targeting KIT and PDGFRA is the frontline therapy for metastatic and unresectable GIST patients. Some initially responsive patients experience tumor progress because of secondary drug resistance, and some cases can develop heterogeneous differentiation. Here we report a rare case of recurrent retroperitoneal extra-GIST with rhabdomyosarcomatous and chondrosarcomatous differentiation with TKI therapy after surgical tumorectomy. Histology, immunohistochemistry, and mutational analysis were performed on primary and recurrent samples. The current case represents the first report of a recurrent retroperitoneal extra-GIST harboring mixed morphologic phenotypes of rhabdomyosarcoma and chondrosarsoma after TKI treatment. The dual differentiation can represent diagnostic pitfall.