Background: Myxoma is a relatively rare mesenchymal tumor seen mainly in the heart and skin. Renal myxomas in particular are exceptionally rare where only 17 cases were previously reported in the English Language literature. Only 2 of the 17 reported cases were located in the renal sinus/pelvis. Case presentation: This is a case of an 18-year-old male patient who complained of right, colicky flank pain associated with abdominal pain and discomfort. Imaging findings revealed right kidney hydronephrosis with a provisional diagnosis of pelviureteric junction (PUJ) stenosis. On computed tomography, there was a very faint thin walled mass abutting the calyces, camouflaged within the dilated renal pelvis. During surgery, a polypoid mass was found at the pelviureteric junction, causing the obstruction. Histological examination showed a hypocellular, paucivascular myxoid neoplasm, with few spindle cells displaying serpentine nuclei and inconspicuous nucleoli. The tumor cells expressed immunoreactivity for vimentin, but not for S100, CD34, actin, or desmin. This will qualify as the third case of renal pelvis myxoma. Conclusion: Myxomas in the renal pelvis/sinus are extremely rare and can present with hydronephrosis and subtle radiological findings mimicking a PUJ stenosis. Being aware of this entity can save the patient unnecessary nephrectomy with possible preservation of the kidney.