Background Inborn errors of immunity (IEI) predispose patients to malignancy, particularly lymphoma, but data on diagnostic sequence and outcomes are limited. Methods We retrospectively analyzed IEI-associated malignancies diagnosed at a single center between January 2004 and December 2025. Results Among 1,668 patients with IEI, 67 (4.0%) developed malignancy. Median ages at IEI and malignancy diagnosis were 8 and 10 years, respectively. Malignancy-first presentation occurred in 45 patients (67%), especially adolescents, and was associated with advanced-stage disease (p = 0.007). Lymphoid malignancies accounted for 90% of cases; non-Hodgkin lymphoma and Hodgkin lymphoma comprised 54% and 36%, respectively, and 84.7% presented with stage III-IV disease. Median event-free and overall survival were 66 and 155 months, respectively. In a clinically selected multivariable Cox model, NHL, solid/plasma cell tumors, older age at malignancy diagnosis, and DNA repair defect status were associated with worse OS. Twelve patients underwent allogeneic HSCT; one died early, and no post-transplant relapses occurred. Conclusion Early immunologic evaluation and timely, individualized consideration of HSCT may support optimized management in children and adolescents, in whom cancer may be the first manifestation of IEI.