It has been shown that children with Duchenne muscular dystrophy (DMD) exhibit specific cognitive deficits. However, the neuropsychological profile has not yet been fully characterized. In order to control for the contribution of motor impairments as a confounding variable that is usually present when assessing children with muscular pathologies, we compared children with DMD to a group of children with an autoimmune pathology that does not entail either brain or cognitive dysfunction but does imply motor impairment: juvenile rheumatoid arthritis (JRA). An extensive neuropsychological evaluation was administered, including intelligence, perception, language, memory and learning, attention, executive function, praxis and reasoning. As the main result, in children with DMD we found significantly lower performances in verbal IQ, verbal short-term memory and phonological abilities, as well as in praxis and executive functioning domains. A wide range of cognitive domains, including verbal abilities, executive functioning, and praxis, must be taken into account when assessing neuropsychological functioning in children with DMD. In particular, subtle executive function impairment could be considered as a subclinical marker of cognitive impairment in developmental disorders.