Objectives: This study investigated the change in suicidal ideation and its risk factors among employees. A longitudinal cohort study was conducted, starting with the baseline online survey in March 2020 (T1), followed by May (T2), and August (T3). The change in suicidal ideation from T2 to T3 and relevant factors associated with suicidal ideation at T3 were examined. Suicidal ideation significantly increased between May and August 2020 among females, younger (under 39 years old), highly educated population, and those without pre-existing mental health conditions. Factors significantly associated with suicidal ideation were younger age, suicidal ideation at T2, and with pre-existing mental health conditions. Loneliness at T2 showed a significant association with suicidal ideation, if adjusting those without pre-existing mental health conditions. National and community support is needed to target people who are likely to be left behind, such as young people and those with pre-existing mental health conditions, in the pandemic. Method: A longitudinal study was conducted with a cohort of full-time employees, starting with the baseline online survey in March 2020 (time point 1), followed by May (time point 2) and August (time point 3). The change in suicidal ideation from time point 2 to 3, and relevant factors associated with suicidal ideation at time point 3, were examined. Results: Suicidal ideation significantly increased between time points 2 and 3 among women, younger people (aged <39 years), those who were highly educated and those without pre-existing mental health conditions. Factors significantly associated with suicidal ideation were younger age, suicidal ideation at time point 2 and pre-existing mental health conditions. Loneliness at time point 2 showed a significant association with suicidal ideation when adjusting for those without pre-existing mental health conditions. Conclusions: National and community support is needed to target people who are likely to be left behind, such as young people, those with pre-existing mental health conditions and those experiencing loneliness, in the COVID-19 pandemic.