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Objectives: Effective treatment of depression is a key target for suicide prevention strategies. However, only around one-third of young people with suicide risk respond to evidence-based treatments. Understanding the trajectory of suicidal ideation, as a marker of suicide risk, over the course of evidence-based treatment for depression might provide insight into more targeted and effective treatments., Methods: This is a secondary analysis of data from the multicentre Youth Depression Alleviation-Combined Treatment trial. A total of 153 young people aged 15-25 years diagnosed with major depressive disorder were randomly assigned in this double-blind, placebo-controlled trial to either cognitive behavioural therapy plus fluoxetine or cognitive behavioural therapy plus placebo. Participants were assessed for depression and suicidal ideation at baseline and at weeks 4, 8 and 12., Results: Using group-based trajectory modelling, we identified two distinct depression trajectories. The first (Improving; 54.9%; n  = 83) comprised those who experienced a consistent decline in depression symptoms. The second (Persisting; 45.1%; n  = 70) comprised those who, despite treatment, still had clinically significant levels of depression by the end of treatment. For suicidal ideation, we identified four distinct trajectories: Non-clinical (15.5%; n  = 20), Low Improving (47.1%; n  = 75), High Improving (24.8%; n  = 38) and High Persisting (12.7%; n  = 20). Treatment allocation was not significantly associated with trajectory membership for either depression or suicidal ideation., Conclusion: Understanding the course of depression and suicidal ideation during treatment has important implications for managing suicide risk. The findings suggest that there is an identifiable group of young people for whom enhanced psychological and/or pharmacological intervention might be required to ensure a better treatment response. Specific interventions for those with suicidal ideation may also be prudent from the outset., Clinical Trial Registration: The Youth Depression Alleviation-Combined Treatment trial was prospectively registered with the Australian and New Zealand Clinical Trials Registry (ACTRN12612001281886).