The objective of the study was to examine the effects of a group-based behavioural, cognitive and skills training intervention (Maltti) provided in schools for elementary school pupils with attention and executive function (EF) deficits. The treatment effects were identified by comparing an intervention group (n = 46) with a waitlist control group (n = 26). Specific effects of the intervention on behavioural deficits in attention and EF in a classroom setting as well as on academic skills were examined. Our analysis indicated that significant intervention effects could be found in the behavioural manifestation of attentional and executive skills in the classroom setting among children (n = 30) who were evaluated as having moderate symptoms in the pre-intervention assessment. Positive effects of the intervention were also observed in arithmetic and reading skills. The severity level of pre-intervention attention and EF deficits did not moderate the results observed in the academic skills tests. The results of this study suggest that a combination of behavioural, cognitive and skills training methods applied in a school context can be effective in reducing attention and EF problems and enhancing the academic performance of children with attention and EF deficits.