The COVID-19 pandemic had caused disruption in each and every sector of daily human life which as well include the education system as students were forced to go through online activities to continue their studies. The effectiveness of the online education system during that period is a matter of concern as recurring disruption caused by another wave of pandemic can hamper the whole education system. Thus, preparedness of educational institutes for another disruption may be required to overcome possible vulnerabilities. This paper conduct analysis on the effectiveness of online education system and its affecting factors with comparison between public and private universities of Bangladesh, based on the data gathered though an online survey (N=357). The effectiveness of online education being a latent variable was measured using the Structural Equation Modeling (SEM) done with the help of SPSS AMOS. From the results it is obvious that factors i.e., student’s perception, their technology acceptance have significant impact on the effectiveness of online learning, but the variation of the impact of these factors are not much significant when comparing between public and private universities in Bangladesh in case of their respective effectiveness.