A 16-month-old intact female Maltese dog was referred for examination of depression and vomiting. Ultrasonography revealed dilated right renal pelvis containing echogenic fluid with free gas. A hyperechoic material suspected of urolith was identified in the right ureter. Computed tomography revealed emphysematous change of the right kidney associated with ureteral obstruction and extrahepatic portosystemic shunt (EHPSS). Ureteronephrectomy and surgical correction were performed for the EHPSS. Escherichia coli was isolated from pus from the right kidney. Quantitative analysis revealed that the urolith was an ammonium urate stone. After 5 months follow-up, no complication was observed. This is the first report of emphysematous pyonephrosis associated with EHPSS in a dog.