The current study examined heterogeneous trajectories of suicidal ideation among homeless youth experiencing suicidal ideation over 9 months in a randomized controlled intervention study. Suicidal homeless youth (N = 150) were randomly assigned to Cognitive Therapy for Suicide Prevention (CTSP) + Treatment as Usual (TAU) or TAU alone. Youth reported their suicidal ideation four times during a 9-month period. We also assessed pretreatment mental health, demographic information and session attendance as predictors of the subgroups, as well as suicide-related factors as outcomes at the 9-month follow-up. Growth mixture models suggested three distinct trajectory groups among youth: Fast Declining (74.7%), Chronic (19.3%), and Steadily Declining (6.0%). Youth in the Chronic group used more substances at baseline than the Steadily Declining group, were more likely to be White, non-Hispanic than the Fast Declining group, and attended more CTSP sessions than other groups. Contrastingly, youth in the Steadily Declining group all experienced childhood abuse. Finally, youth in the Chronic group showed significant higher risk for future suicide compared to those in the Fast Declining group at 9 months. Findings support the heterogeneity of treatment responses in suicide intervention among homeless youth, with implications to improve treatment efforts in this very high-risk population.