Background: Increasing prevalence rates for suicidal ideation among university students call for better understanding of critical risk factors. Because of traditional masculinity ideologies (TMI; socially defined sets of standards and norms how men are expected to be or behave), men are less likely to report suicidal ideation but up to four times more likely to die by suicide. Establishing low-threshold risk factors to identify suicidal ideation among male students at an early stage is paramount. Study dropout thoughts, due to a particular relationship with TMI, could be one such risk factor. The present study therefore examines the relationship between study dropout thoughts and suicidal ideation as well as gender-differences in risk patterns. Methods: A total of N = 4894 German university students (24.6% men) completed a cross-sectional online survey on mental health at the University of Cologne. A first part of the survey consisted of sociodemographic and study related questions (e.g., study dropout thoughts). In the second part psychological syndromes (any psychological syndrome, depressive syndrome, alcohol syndrome), life stressors and suicidal ideation were assessed using the Patient Health Questionnaire D (PHQ-D). Results: Male university students expressed study dropout thoughts more frequently than female students, while for both genders study dropout thoughts were associated with increased suicidal ideation. Significant gender-differences were observed for all outcomes, with financial stress and a recent bad experience being risk factors for suicidal ideation in men but not women. Relationship problems, problems at work, and current psychotherapy use were associated with increased suicidal ideation in women but not in men. Conclusions: In the University context, study dropout thoughts are expressed often, especially by male students. Given that study dropout thoughts are associated with suicidal ideation and that male-specific risk patterns for suicidal ideation have been identified, men who report thoughts of dropping out of studies or experience financial stress should be screened for suicidality and mental health problems. Future prevention measures in the University context should consider study dropout thoughts and male-specific risk-patterns to increase chances for detection of male students at risk for suicide and to improve the effectiveness of suicide prevention programs specifically targeting men.