Background: Prior research indicates that the factors that trigger suicidal ideation may differ from those that maintain it, but studies into the maintenance of suicidal ideation remain scarce. Our aim was to assess the longitudinal course of suicidal ideation, and to identify predictors of persistent suicidal ideation. Methods: We used data from the Netherlands Study of Depression and Anxiety (NESDA). We performed a linear mixed-effects growth model analysis (n = 230 with current suicidal ideation at baseline) to assess the course of suicidal ideation over time (baseline through 2-, 4-, 6- and 9-year follow-up). We used logistic regression analysis (n = 195) to test whether factors previously associated with the incidence of suicidal ideation in the literature (insomnia, hopelessness, loneliness, borderline personality traits, childhood trauma, negative life events) also predict persistence of suicidal ideation (i.e., reporting ideation at two consecutive assessment points, 6- and 9-years). We controlled for socio-demographics, clinical diagnosis and severity, medication use, and suicide attempt history. Results: Suicidal ideation decreased over time, and this decrease became slower with increasing time, with the majority of symptom reductions occurring in the first two years of follow-up. More severe insomnia and hopelessness were associated with increased odds of persistent suicidal ideation, and hopelessness was a significant mediator of the relationship between insomnia and persistent suicidal ideation. Limitations: Findings may not generalize to those with more severe suicidal ideation due to dropout of those with the worst clinical profile. Conclusions: Targeting insomnia and hopelessness in treatment may be particularly important to prevent the persistence of suicidal ideation.