System implemented within an organization has a role of improving its efficiency, effectiveness and productivity. Nevertheless, sometime an Information System can not affect the organization on the desired way, due to its improper planning and design. Such a systems might operate for several years without having a major positive effect. Therefore, every organization have to evaluate their IT systems timely, to ensure their effectiveness and efficiency. HEMIS is one of such a systems operating since 2011, in the environment of the Ministry of Higher Education of Afghanistan, with out having a major positive impact. This work evaluates and analyses HEMIS, it identifies its issues, challenges and reasons of its ineffectiveness. And provides a new concept for the solution of the respected challenges.