Background Cystinosis is a rare autosomal recessive disease. Children with nephropathic cystinosis (NCTN) have evidence of intellectual dysfunction and behavioural abnormalities which are attributed to renal dysfunction, metabolic disarrangement, and gene mutation. This study aimed to characterize the cognitive functions and behavioural profiles in nephropathic cystinosis patients on cysteamine therapy, and determine its relation to cysteamine treatment duration. In this analytical cohort study, 20 children with nephropathic cystinosis aged 6 years or above were compared to 26 children with chronic kidney disease (CKD) matched in age, sex, and CKD stage. All patients were subjected to full clinical and psychometric assessment using the Child Behaviour Checklist (CBCL) and the Arabic language version of Stanford-Binet test (SB). Results There was no significant difference between both groups regarding Stanford-Binet test (SB) and Child Behavioural Checklist (CBCL), apart from delinquent behaviour. Duration of cysteamine treatment was inversely correlated with short-term memory, thought, and sex problems. Conclusions Children with cystinosis have a wide range of neurocognitive and behavioural problems that still present after cysteamine treatment and may be related to impact of genetic mutation on brain structure and function. Longer duration of cysteamine treatment could have beneficial effects on some behavioural problems.