Background Inconsistent results on neuropsychological outcome in patients treated for acyanotic congenital heart disease (aCHD) questioned the clinical relevance of possible neurobehavioral sequelae in this group. This study was designed to objectify the neuropsychological profile and evaluate associations with medical data. Methods Patients with a corrected atrial or ventricular septal defect, ASD-II or VSD, (n =46; mean age 9 years, 2 months) and a matched control group were submitted to an intelligence test (Wechsler Intelligence Scale for Children, third edition, Dutch version) and evaluated with a neuropsychological test battery (Developmental Neuropsychological Assessment, second edition, Dutch version). Hospitalization variables were retrieved to evaluate associations with cognitive outcome. Parents completed a behavioral checklist (Achenbach Child Behavior Checklist for Children aged 6–18). Results ASD-II patients showed lower scores in domains of visuospatial processing, language, attention, and social perception. VSD patients displayed subtle problems in attention and visuospatial information processing. Only few perioperative medical factors, but also socioeconomic variables were associated with cognitive outcomes. Parents of ASD-II patients reported more school problems when compared to controls. Conclusions After treatment for aCHD, subtle cognitive difficulties can present in domains of visuospatial information processing, language, attention, and social perception. These shortcomings might hamper school performances, as is suggested by lower school competence ratings. Ongoing follow-up and cognitive screening is warranted to promote developmental progress, in which both parents and clinicians share responsibility.