Shift work does not synchronize with the 24-hour human circadian rhythm, so shift workers experience various problems related to this disruption. This study investigated the relationship between suicidal risk and emotional difficulties such as depression and anxiety in shift workers according to gender. We analyzed data collected from 79,009 health checkup recipients. We checked psychosocial factors for different genders using the Chi-square test and t-tests. To examine the relationship between shift work and suicidal ideation, we estimated an odds ratio after adjustment for age, depression, and insomnia. There was no difference in terms of the risk of suicidal ideation between shift workers and day workers among women (adjusted odds ratio [AOR], 0.957; 95% confidence interval [CI], 0.826–1.109), whereas the risk of suicidal ideation was significantly higher for shift workers than for day workers among men (AOR, 1.157; 95% CI, 1.021–1.310). This study confirmed that associated factors of shift work-related suicidal ideation could act differently by gender. Shift work for women is generally associated with emotional difficulties such as depression and anxiety, whereas maladaptation to shift work may be related to suicidal ideation among men. A gender-specific suicide prevention approaches will be needed for shift workers.