Neurocognitive impairments and neuroimaging abnormalities are frequently observed in adults with systemic lupus erythematosus. There is a paucity of similar data in childhood-onset disease. We hypothesized that neurocognitive and neuroimaging abnormalities would be prevalent in children undergoing neuropsychological evaluations. We reviewed patient neurocognitive evaluations performed at a large United States pediatric institution during the period 2001 to 2008. Records were retrieved from 24 children referred to neuropsychology due to clinical indications. Data from 15 children enrolled in a prospective structure-function association study were also analyzed. Subjects were predominantly African-American and Hispanic adolescent girls of average intelligence. aPL positivity and aspirin use was prevalent. Neurocognitive impairment was designated in 70.8% of retrospective, and 46.7% of prospective cohort patients. Deficits were seen at times of wellness, without previous neuropsychiatric lupus, and early in disease courses. Scores >1.5 standard deviations below published age-matched norms were common in tests of executive functioning, visual memory and visual-spatial planning. Features of depression were seen in 33.3% of the children in the retrospective cohort (clinical referrals). Cerebral and cerebellar volume loss was observed in a majority of blinded prospective cohort research magnetic resonance images (73.3% and 67.7% respectively). White matter hyperintensities were observed in retrospective and prospective cohort magnetic resonance images (36.6% and 46.7% respectively). Larger prospective studies that elucidate structure-function associations in children with systemic lupus erythematosus are planned.