Suicidal behavior increases substantially during early adolescence, a critical understudied developmental period. This study reports on the prevalence of suicidal ideation, suicide attempts, and course of suicidal ideation among Puerto Rican early adolescents, a high-risk group for suicidal behavior in adulthood. Gender differences and the prospective association of psychiatric disorders with course of suicidal ideation are examined. Participants were 1228 Puerto Rican adolescents (ages 10–13 at wave 1; 48% female) and parents, selected through probability-based sampling, assessed yearly across three waves. Adolescents and parents reported via Diagnostic Interview Schedule for Children-IV about 12-month suicide attempts and suicidal ideation (further categorized as never present, onset, recurrence, and remission), mood and anxiety disorders; parents reported on disruptive disorders. Over the three waves, 9.5% early adolescents thought about suicide and 2.1% attempted suicide. In adjusted multinomial regression models, compared to those with never present suicidal ideation, female gender was related to onset of suicidal ideation (OR = 2.60; 95% CI, 1.22–5.55). Disruptive disorders were related to onset (OR = 5.80; 95% CI, 2.06–16.32) and recurrence of suicidal ideation (OR = 5.07, 95% CI, 1.14–22.47), mood disorders were related to remission (OR = 14.42, 95% CI, 3.90–53.23), and anxiety disorders to onset of suicidal ideation (OR = 3.68, 95% CI, 1.75–7.73). Our findings inform strategies tailored for early adolescents. To address onset of suicidal ideation, prevention should focus on girls and those with anxiety or disruptive disorders. When ideation is recurrent, interventions oriented to reduce disruptive behavior and its consequences may help achieve remission.