This is the first attempt to conduct cost analysis of the online learning in Mongolia. The online course development cost varies by Higher education institutions and countries due to the different methodologies and labor costs.The cost analysis revealed that traditional classroom learning is expensive than online learning. In the example of the particular course of the Mongolian National University Medical Sciences, we estimated that online learning is more cost-effective than traditional learning by 152.51 units. If we add student learning cost, the estimate revealed that online learning is more cost-effective than traditional learning by 6002.7 units. Online and traditional students' learning achievements are not significantly different according to the results of the parametric (Levene's test) and non-parametric (Mann-Whitney test) methods in the example of 2 courses.Implications for practice and/or policy. The cost effectiveness analysis is powerful decision-making tool. This study serves as an evidence to policy makers, and higher education manager.