Background: Malignant granular cell tumor (GCT) is extremely rare. Malignant GCT with EP300 gene mutation in the bladder has not been reported in the literature. Case Presentation: We report a special case of 45-year-old female with malignant GCT of the bladder. Pathological examination showed that the mass was 11 × 11 × 4.5 cm in size, involved in the bladder’s posterior wall. Under the microscope, the tumor cells were arranged in the shape of a nest or cord to infiltrate the bladder’s wall. The tumor cells were pleomorphic, red-stained granular within the cytoplasm, with increased nuclear/cytoplasmic ratio, vacuolar nuclei, and obvious nucleoli. The tumor cells were showed obvious nuclear atypia, and the mitosis was more than 5/50HPF. Coagulative necrosis was widely showed within the tumor. Immunohistochemistry (IHC) showed that S-100, NSE, CD68, CR, α-AT, and TFE-3 were strongly positive, and the Ki-67 proliferation index was around 15%. The next-generation high throughput sequencing indicated that EP300 gene was missense mutated (c.457A > G) with 33% mutation abundance, and genes of DPYD (c.1627A > G), ERCC1 (c.354T > C), NQO1 (c.559C > T), TPMT (c.719A > G) and XRCC1 (c.1196A > G) were polymorphic mutated. The patient died after three months of the second surgical treatment. Conclusions: We report for the first time a primary bladder malignant GCM accompanied by mutations in special driving genes such as EP300. We also conducted a comprehensive literature review and an in-depth discussion.