Objectives: To evaluate the impact of COVID-19 pandemic on the mental health of Malaysian university and pre-university students, especially after the shift to online academic activities, following almost one year of experiencing the pandemic Methods: A cross-sectional online survey was conducted among Malaysian pre-university and university students, nationwide, using perceived stress scale-10 questionnaire and another validated 11-construct questionnaire. Key findings: : The online questionnaires were filled out by 383 Malaysian pre-university and university students. About 40% of the respondents reported moderate to severe level of loneliness and social isolation. There was a significant correlation between suicidal thoughts and the social isolation. The prevalence of moderate to severe suicidal thoughts (14% of the respondents) was more than the reported prevalence before COVID-19 pandemic. The residential state, gender and ethnicity of the respondents did not show an association with depressive and suicidal thoughts of the respondents. Conclusion Loneliness and feeling social isolation were the most prevalent problems, as reported by the students. Suicidal Thoughts are more prevalent, compared to pre-COVID-19 reports. The educators and institution managers must seek for appropriate methods to address the critical condition.