Deficiency of DNA mismatch repair (MMR) induces micro-satellite instability (MSI). Pembrolizumab, an antibody targeting PD‐1 (an immune checkpoint inhibitor), is more effective against MMR‐deficient tumours than against MMR‐proficient tumours. The status of MMR is a useful biomarker for predicting the effectiveness of pembrolizumab administration. Although the status of MMR has attracted attention in skin tumours, there are few reports on MSI in extramammary Paget's disease (EMPD). MSI testing showed the occurrence rates of MSI‐high (more than two markers are unstable), MSI‐low (one marker is unstable) and MSS (all markers are stable) tumour tissues were 0% (0/101), 1.0% (1/101) and 99.0% (100/101), respectively. The status of MMR may not be useful for the potential therapeutic application of pembrolizumab.