SummaryMyelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN) overlap syndromes show a male predominance and men with MDS/MPN have worse outcomes, but it is unknown if the mutational burden differs between genders. We reviewed 167 patients with MDS/MPN and found that men had worse overall survival [hazard ratio (HR) 2·09, 95% confidence interval (CI) 1·16–3·75; P = 0·013] independent of subtype, Revised International Prognostic Scoring System score and age at diagnosis. We analysed the genomic data of a subset of 100 patients. Men had 0·88 more somatic mutations on average (95% CI 0·20–1·56, P = 0·011) independent of subtype, sample source and blast percentage. More somatic mutations was associated with a higher incidence of transformation to acute myeloid leukaemia (subdistribution HR 1·30, 95% CI 1·01–1·70; P = 0·046). Men had 0·70 more mutations in high‐risk genes [additional sex combs like‐1 (ASXL1), enhancer of zeste homolog 2 (EZH2), Runt‐related transcription factor 1 (RUNX1), SET binding protein 1 (SETBP1), NRAS proto‐oncogene, GTPase (NRAS), stromal antigen 2 (STAG2)] on average (95% CI 0·11–1·29, P = 0·021), and 13‐times higher odds of harbouring an EZH2 mutation (95% CI 1·64–102·94, P = 0·015). The presence of an EZH2 mutation was associated with worse survival among men (HR 2·98, 95% CI 1·1–8·0; P = 0·031). Our present findings suggest that the worse outcomes in men with MDS/MPN are associated with a higher number of somatic mutations, especially in high‐risk genes. These results warrant validation in larger cohorts and investigation of the underlying mechanisms.