Incidence, molecular presentation and outcome of acute myeloid leukaemia (AML) is influenced by sex, but little attention has been directed at untangling sex-related molecular and phenotypic differences between female and male patients. While increased incidence and poor risk is generally associated with a male phenotype, the poor prognostic FLT3 internal tandem duplication (FLT3-ITD) mutation and co-mutations with NPM1 and DNMT3A is overrepresented in female AML. Here, we investigated the relationship between sex and FLT3-ITD mutation status by comparing clinical data, mutational profiles, gene expression and ex vivo drug sensitivity in four cohorts: BeatAML, LAML-TCGA and two independent HOVON/SAKK cohorts, comprising 1755 AML patients in total. We found prevalent sex-associated molecular differences. Cooccurrence of FLT3-ITD, NPM1 and DNMT3A mutations was overrepresented in females, while males with FLT3-ITDs were characterised by additional mutations in RNA splicing and epigenetic modifier genes. We observed diverging expression of multiple leukaemia-associated genes as well as discrepant ex vivo drug responses, suggestive of discrete functional properties. Importantly, significant prognostication was only observed in female FLT3-ITD mutated AML. Thus, we suggest optimisation of FLT3-ITD mutation status as a clinical tool in a sex-adjusted manner, and hypothesize that prognostication, prediction and development of therapeutic strategies in AML could be improved by including sex-specific considerations.