Rheumatoid arthritis (RA) is a multifaceted autoimmune disorder with notable gender differences. The impact of gender-specific genetic variations on RA's pathogenesis remains unclear. This research investigates gender-specific genes in RA using Mendelian randomization (MR) and transcriptome sequencing to understand RA mechanisms, focusing on gender-specific immune responses. We used the limma package to analyze gender-differential genes in RA patients, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses. Key genes were identified through least absolute shrinkage and selection operator and support vector machine recursive feature elimination, and a diagnostic nomogram was constructed and validated using the gene expression omnibus database. Immune cell and function analyses were performed using single-sample gene set enrichment analysis, and a competing endogenous ribonucleic acid (RNA) network was constructed. MR analysis was used to investigate the causal relationship between gender-differential genes and RA. Thirty differentially expressed genes were identified, with Gene Ontology analysis indicating their involvement in neutrophil-mediated killing. Six key genes (MAP7D2, AR, DNAH6, CXorf36, ORM1, and IQGAP3) were identified, and a diagnostic nomogram was developed (area under the curve: 0.956 in the training set, 0.859 in the validation set GSE68689). Furthermore, single-sample gene set enrichment analysis analysis indicated higher immune cell infiltration in female RA patients, highlighting gender's influence on immune response. The competing endogenous RNA network revealed potential RNA regulatory pathways. MR analysis found that the RETN gene has a specific role in seronegative RA patients, particularly in females. This study enhances the understanding of RA's gender-specific pathogenesis and offers a foundation for future personalized treatment and prevention strategies, aiding in developing more effective individualized treatment plans for RA patients.