Background The involvement of the central nervous system is not rare in rheumatoid diseases. Even though children with juvenile idiopathic arthritis (JIA) may face academic difficulties until adulthood, very few studies have evaluated potential cognitive disorders in these patients. The present research aims to thoroughly investigate the cognitive and neuropsychological functioning of these patients. Methods We measured the cognitive profile of JIA patients via their neuropsychological profile, implicit memory and social cognition skills, and estimated their academic performance using reading and mathematics tests. We recruited 21 children with JIA aged 6 to 17 years-old (M = 11.01, SD = 3.30) and 21 healthy children matched in age, gender, academic level (same school class) and socioeconomic status. Results Our results showed that the cognitive profile and estimated academic ability of JIA patients are similar to those of their peers. These results support the hypothesis that children with JIA have the same cognitive predispositions to succeed at school as any other pupil. Conclusion Comparing our results with the existing literature, we propose complementary hypotheses for further research. Longitudinal studies seem to be necessary to understand the psychosocial and cognitive processes involved in the development of children with JIA.