The physical classroom learning nowadays is no longer applicable for the current younger generations. Internet and distance learning which is generally known as online education plays a vital roles in the country’s education system. It is undeniable that online education provides ample of benefits to young learners. Nevertheless, there are also many negative implications from online education. Limited collaborative learning, increase in time and effort are the several negative implications from online education. This study examines the implications of online education among students especially in a private higher learning institution and its effect towards Malaysian national education system. Information has been collected through surveys, interviews and together with secondary data, and were seen using SPSS. The studies found that there are various serious issues regarding online education and on its effect on the quality of Malaysian Education System to certain extend. Several problems have been identified and these issues have to be solved in order to sustain the quality of education for future generations. Furthermore, Ministry of Higher Education (MOHE) should formulate a standard policy, monitor closely the implementation of online education, evaluate and review the method used in teaching and upgrade to maintain the quality of online education in private higher education institution.