Violations of children rights are the grey areas in Pakistan that have grave consequences for the educational progress of students especially those studying at elementary level. This study probes the major children rights contravention at elementary level schools located in Pakistan; particularly in government sector schools where the learning course is usually taken by the principals and teachers as a regular affair without any fervent approach. In order to investigate the state of children rights in schools, principal, teachers and students from rural and urban area public sector institutions of Capital Territory Islamabad were taken as the sample for this study so that the state of these institutions in terms of providing basic rights to elementary students could be analyzed and it could be seen if they affect the performance of children in class or not. The result indicates the prevalence of several nuisance areas including corporal punishment, bullying, unhygienic environment, lack of educational facilities and proper infrastructure in these institutions which are directly affecting the performance of children in form of a decline in learning outcomes, specifically in rural areas where the use of physical punishment is reported to be practiced more in ratio as compared to urban areas. The study is significant as it explores issues and causes for children rights violations and suggests the necessary measures that would make the learning environment more conducive for students.