Congenital heart disease occurs in approximately 9 out of 1,000 newborns. Early cardiac corrective surgery is often associated with partial or total thymectomy. The long-term effects of early thymectomy on the subsequent development of the immune system in humans are not fully known. Some studies have found that total T cell, CD4+- and CD8+- T cell populations were decreased in thymectomized patients compared to controls, whereas cell numbers were similar in some studies. Studies also show that T cell levels and subgroups change according to the time elapsed since thymectomy. A 13-month-old female patient was presented with a history of premature birth followed up at the pediatric cardiology outpatient clinic due to a ventricular septal defect, patent ductus arteriosus, and tricuspid insufficiency. At 9 months of age, the patient had undergone cardiac corrective surgery with partial thymectomy. Postoperatively, the patient had a history of multiple hospitalizations and antibiotic use due to recurrent lung infections. Flow cytometric lymphocyte analysis showed decreased CD3+ T cells: 47% (n: 51–81.8), CD4+ T cells: 12% (n: 27.6–55.6), recent thymic emigrant T cells 18.5% (n: 42.5–82.2), and mildly elevated CD8+ T cells: 34% (n: 12.7–30.9). This case report aims to contribute to the literature and to inform clinicians about the coexistence of congenital heart disease and transient immunological abnormality by presenting our patient, who had a history of thymectomy due to cardiac corrective surgery.