Health information technology systems have the capacity to improve health outcomes for the patients thus ensuring quality and efficient services. Health information systems (HIS) are important tools in guidance towards patient safety and better outcomes. However, still, morbidity and mortality attributed to medical errors remain an important issue that needs to be addressed. The objective of the present study was to assess the health information system in terms of technological, environmental, organizational and human factors affecting the adoption as well as the perceptions of stakeholders along with barriers and constraints related to successful implementation. A descriptive cross-sectional study design was used. Prospective data was collected from primary sources by self-administering the pre-validated questionnaires as well as by physical verification of the availability of equipment. After data collection, data was analyzed to assess the health information management systems. The results of the present study showed that the health information system in Pakistan is not up to the mark. The equipment was mostly unavailable at the primary healthcare facilities. The staff was also unsatisfied with the available services. Administrative, financial and human constraints were identified as the major barriers towards successful implementation and management of HIS. The present study concluded that the health information system of Pakistan needs to be revamped. Health information management system partially existed at district and sub-district offices, while was completely absent at tertiary, secondary and primary healthcare levels. The poor adoption of health information technology systems at healthcare facilities might largely be attributed to insufficient human resources with limited resources and budget allocation for health in Pakistan. Effective and timely strategies involving all important stakeholders and healthcare professionals must be designed and implemented at the National level to restructure an affordable, resilient and quality healthcare system.