Implementation of technological innovation projects particularly Information Technology (IT) projects for health care and training service in developing countries faces challenges. ALERT hospital and training center currently implementing IT projects such as eHealth and eLearning to improve the quality of health care and deliver effective training to health professionals respectively. However, to develop and implement eHealth and eLearning in the healthcare and training system it is still challenging because the technological innovations by very nature are complex. These challenges of implementation include financial, infrastructure, knowledge, behavioral and social context, technological, leadership and governance, security, and stakeholders. The main purpose of this study is to assess the implementation challenges and understand mitigation ways. Under this imperative, the study answers the following question â€œwhat are the implementation challenges and mitigation ways to alleviate the implementation barriers?â€. Qualitative and quantitative approaches have been employed in this study. The quantitative survey result shows that there are challenges of infrastructural, financial, behavioral, and social context, technology, stakeholders, and knowledge per their magnitude of prevalence. Other challenges such as the issues of COVID-19, staff turn-over, monitoring and evaluating, electric power availability, conflict of interest between stakeholders, accessibility, and language, and computer literacy of beneficiaries are also implementation challenges. Besides the qualitative study result identified that there is a good practice of mitigating the challenges of security and leadership and governance factors. In the future contemporary effects and issues of COVID on IT projects for health and training service implementation should further be investigated. Besides security, leadership and governance are not severe challenges in this study hence in the future, these factor variables should be more studied.