Overlap syndrome is the combination of autoimmune liver diseases, and this term usually describes the coexistence of autoimmune hepatitis (AIH) and primary biliary cirrhosis (PBC) in the same patient. Membranous nephropathy (MN) is the most common pattern of idiopathic nephrotic syndrome in patients without diabetes. The coexistence of PBC-AIH overlap syndrome and MN is very rare. Herein, the patient we describe exhibited large amounts of proteinuria and hepatic dysfunction nearly at the same time. We administered azathioprine to our patient. Fortunately, the patient demonstrated a good response to azathioprine, including a partial reduction in proteinuria from ~ 12.5 g/D to 2.62 g/D after 21 months of observation and the improvement of liver function. Our findings suggest that azathioprine may be a suitable treatment option for patients presenting with coexisting PBC-AIH overlap syndrome and MN.