Background Children with intellectual development disorder (IDD) have high rates of comorbid neuropsychological and behavioural problems. However, there are not many studies on this population in middle-income and low-income countries. Therefore, we aimed to investigate the prevalence of neuropsychological and behavioural problems in students with and without IDD and to assess the correlation between the responses from informants (parents and teachers) and the clinical diagnoses in Brazil. Methods After clinical diagnosis, 78 male and female students (7-15 years old) were divided into two groups: children with IDD (n = 39) and children without IDD (n = 39). The Child Behaviour Checklist (CBCL) and Teacher's Report Form (TRF) scales were used to track neuropsychological and behavioural problems. Calculations of prevalence ratios were performed using Poisson regression with Wald tests. The CBCL and TRF results were compared between groups with Mann-Whitney U-tests and receiver operating characteristic (ROC) analyses. The agreement between scales was assessed using the Spearman correlation test. Results Neuropsychological and behavioural problems were significantly more prevalent in students with IDD. The average amount of CBCL problems was significantly higher than that of TRF in the dimensions of thought, attention, somatic, attention deficit/hyperactivity, opposition defiant and total problems. Low-to-moderate correlations between CBCL and TRF dimensions in the IDD group were observed. ROC analyses revealed that the dimensions of internalising problems and total scores reflecting CBCL and TRF problems were the most important factors for identifying neuropsychological and behavioural problems in the IDD group. Conclusions Students with IDD require early identification of behavioural and emotional symptoms to avoid the underdiagnoses of various mental health problems, especially those with internalising characteristics. The CBCL and TRF may assist in the early screening of these comorbidities.