Objective To evaluate the clinical value of CD4⁺ cell percentage (CD4⁺%) and NK cell percentage (NK%) in predicting treatment outcomes in children with aplastic anemia (AA), providing a reference for precise diagnosis and treatment. Methods This retrospective study analyzed the clinical data of AA children treated with cyclosporine A at the First Affiliated Hospital of Xinjiang Medical University from January 2019 to April 2024. The study involved 48 AA children as the observation group and 50 children undergoing medical check-ups during the same period as the control group. Lymphocyte subset data were collected from both groups to analyze differences and their relationship with treatment efficacy. Based on hematological responses, the observation group was divided into an effective group of 18 patients (HR group, including complete and partial remission) and an ineffective group of 30 patients (NHR group, including non-remission). Results Univariate analysis showed that NK% in the observation group was significantly lower than that in the control group (P<0.05). The observation group was followed up for 3 months. The HR group had a lower CD4⁺% than the NHR group (P=0.018) and a higher NK% than the NHR group (P=0.029). Multivariate logistic regression analysis indicated that a high CD4⁺% was a risk factor for poor treatment efficacy (OR=1.062), whereas a high NK% was a protective factor (OR=0.820). The area under the curve for the prediction of HR in pediatric AA by combining CD4⁺% and NK% was 0.812. Conclusions A higher CD4⁺% at diagnosis is a predictor of poor treatment response, whereas a higher NK% is associated with better outcomes.