Although the COVID-19 pandemic which strikes Malaysia has now entered the endemic phase, the implications from it remain especially in mental health aspects. Students are a group that is at risk of experiencing stress due to the changes that occurred in the educational system. Therefore, this study was conducted to investigate the impact of online learning on students’ stress during pandemic COVID-19 in Universiti Sains Islam Malaysia. The total number of respondents involved was 360 students. The Student Stress Inventory (SSI) has been used to identify the level of student’s stress among undergraduate students. Descriptive statistical analysis in the form of percentage frequency, Pearson correlation and t-test were conducted using the Statistical Package for the Social Sciences (SPSS) Version 26 software. Analysis showed that majority of the student had moderate stress score of student stress as the results of online learning. Independent t-test was used to identify the gender differences in terms of stress as a result of online learning. This study shows there was significant difference between males and females in aspect stress. Besides that, the study was concluded that there was significant impact and small effect on students’ academic achievement before and during Movement Control Order. The implication of the study, suggestions, and future direction was also discussed.