Although carcinoembryonic antigen (CEA) and cytokeratin 19 fragment (CYFRA) are useful marker for extramammary Paget's disease (EMPD), the serum CEA and CYFRA levels are not elevated in most EMPD patients without metastasis. Therefore, further useful biomarkers are needed for the detection of EMPD including early lesions. Cell‐free DNA (cfDNA) has attracted attention as an indicator of clinical conditions in several cancers, and we studied the clinical implications of cfDNA for EMPD. The serum cfDNA levels were significantly elevated in EMPD patients with or without metastasis compared to those in healthy controls. And serum cfDNA was a better diagnostic marker for the presence of EMPD compared to serum CYFRA. Moreover, the post‐operative serum cfDNA levels were significantly lower than those from the pre‐operative samples, and the change in serum cfDNA levels reflected the clinical courses of EMPD patients treated with chemotherapy. Taken together, serum cfDNA levels may be useful marker for the diagnosis and disease progression in EMPD.