Extramammary Paget disease (EMPD) is a rare malignancy of the skin. Because of the scarcity of the cases, genomic alterations in EMPD are poorly characterized. To address this issue, we have interrogated 39 EMPD samples and patients blood with exome sequencing. The mutational load of EMPD was moderately high; the median prevalence of somatic mutations was above 3 mutations per megabase, a number comparable to the one of kidney renal cell carcinoma. Our study identified several putative driver events. ERBB2 mutation, as well as amplification, is frequent in our samples and likely the key driver of EMPD. The mutations are enriched in the tyrosine kinase domain of ERBB2, and are likely to cause functional alteration of the gene product. This observation is in line with previous papers reporting the efficacy of trastuzumab for EMPD. Other cancer genes including ERBB3, KMT2C, MLL4, and COL1A1 are also frequently mutated in EMPD. Driver mutation analysis by OncodriveFM identified potential novel cancer genes that are previously unreported in other cancer types. Copy number analysis identified recurrent somatic copy number aberrations. Frequent deletion peaks included CDKN2A and TSC2, both of which were important tumor suppressor genes. Mutational signature analysis showed that APOBEC3B activation, coupled with aging, was driving the somatic mutations in EMPD. We also identified evidence of APOBEC3B activation including kataegis and strand bias in the EMPD genome. In conclusion, our study provides the comprehensive landscape of somatic mutations in EMPD as well as insights into the mechanisms behind the carcinogenesis of EMPD. We have identified putative driver mutations including ERBB2 and ERBB3, which are readily targeted. We also suggest that EMPD may be treated with cancer immunotherapy, for the moderately high mutational load observed in EMPD is associated with the response to cancer immunotherapy in other cancer types. These insights provide rationale for use of systemic treatments in patients with EMPD.