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Objective: Gout‐related comorbidities are intricate and its clinical features may demonstrate sex difference; however, few studies have evaluated the links between comorbidities and gout in a female population. The objectives of this study were to compare the aggregation and transitive trajectories of comorbidities of gout, and their consequences in female and male gout populations. Methods: A prospective cohort study was conducted using data from the Taiwan National Health Insurance Research Database. A female and male gout population were followed up from 2000 to 2009 to identify the comorbidities of cardiovascular disease, hyperlipidemia, hypertension, diabetes mellitus (DM) and chronic kidney disease. The cumulative incidence of stroke from 2000 to 2010 was examined. A latent trajectory analysis was used to determine the transitive trajectories of the comorbidities of gout. Results: Both female and male patients with gout had five risk cluster transition (CT) phenotypes of comorbidities within 10‐year follow‐up: CT1 and CT2, with various persistent comorbidities; CT3, with few persistent comorbidities; and CT4 and CT5, with transfer to cluster 1 from other clusters. The female participants in CT2 predominantly experienced DM and were associated with significantly increased risk of developing stroke. Conclusion: Diabetes is a notable risk factor for the development of stroke in female patients with gout. Early assessment and management for the comorbidities of gout, particularly in DM, would effectively reduce future stroke risk in female gout population. [ABSTRACT FROM AUTHOR]