Previous studies have reported increased rates of social difficulties in children treated by haematopoietic cell transplant (HCT). This study assessed social functioning in children with congenital immunodeficiency treated by HCT and investigated two potential underlying mechanisms that may explain social difficulties: executive function skills and physical appearance. In total, 31 children (8-16 years of age) were assessed on measures of social functioning and peer relationships, executive function and physical appearance. Results were compared with a control group of 31 healthy children, matched for age, gender, ethnicity and cognitive ability. Parent, teacher and self-report data were collected. HCT survivors were described by parents and teachers, but not by themselves, as experiencing more difficulties with social functioning than the control group. Executive function was not associated with social functioning. However, an objective measure of physical appearance was significantly associated with social functioning. Results suggest that children treated by HCT for congenital immunodeficiency do experience significant difficulties in social functioning, not solely accounted for by below average intelligence. These difficulties are associated with physical appearance, but not with executive functional skills. This has clinical implications for identifying and treating children at increased risk of difficulties with social functioning.