Type II Abernethy malformation is an extremely reported congenital extrahepatic portosystemic shunt in complication with nephrotic syndrome. We present the case of an 8-year-old boy who presented with symptoms of type II Abernethy malformation and nephrotic syndrome. This diagnosis of this type II Abernethy malformation was based on physical examination, blood tests, urinalysis, nephrotic and hepatic function tests, routine clinical lipid measurements, abdominal ultrasonography, and computed tomographic angiography. A kidney biopsy revealed the pathological features of nephrotic syndrome. This is the second reported patient diagnosed with type II Abernethy malformation and nephrotic syndrome. Captopril treatment was effective in improving the symptoms of this case. A patient with type II Abernethy malformation related to immune complex-mediated glomerular injury was effectively improved with medication. Type II Abernethy malformation is a causative factor of immune complex-mediated glomerular injury in nephrotic syndrome. Captopril treatment significantly improved the symptoms in this case.