Background Renal cell carcinoma (RCCs) is the most common malignancy of the kidney. When RCC progresses, it is known to form tumor thrombus in the renal vein and/or inferior vena cava. However, RCC does not normally form tumor thrombus in the pelvicalyceal system. Case presentation A 56-year-old man presented to our department for the treatment of a renal tumor with asymptomatic gross hematuria. In a dynamic CT study, contrast enhancement revealed a tumor suspected to be RCC, but atypical finding as a tumor thrombus that filled the pelvicalyceal system was also observed. Nephroureterectomy was performed, and the tumor was diagnosed histopathologically as clear cell RCC and papillary RCC. Conclusion We report a rare case of RCC directly invading the pelvicalyceal system as a thrombus mass, with no microscopic individual tumor implants in the pelvicalyceal system wall, invasion of the renal vein, or invasion of adjacent organs. To our knowledge, only six such cases have been reported in English literature, and as a result, very few theories explaining pelvicalyceal system invasion have been presented. This highlights the significance of adding invasion of the pelvicalyceal system as part of the most recent, updated tumor metastases classification.