Background Approximately 70% of mental health disorders appear prior to 25 years of age and can become chronic when ineffectively treated. Individuals between 18 and 25 years old are significantly more likely to experience mental health disorders, substance dependencies, and suicidality. Treatment progress, capitalizing on the tendencies of youth to communicate online, can strategically address depressive disorders. Objective We performed a randomized controlled trial (RCT) that compared online mindfulness-based cognitive behavioral therapy (CBT-M) combined with standard psychiatric care to standard psychiatric care alone in youth (18-30 years old) diagnosed with major depressive disorder. Methods Forty-five participants were randomly assigned to CBT-M and standard care (n=22) or to standard psychiatric care alone (n=23). All participants were provided standard psychiatric care (ie, 1 session per month), while participants in the experimental group received an additional intervention consisting of the CBT-M online software program. Interaction with online workbooks was combined with navigation coaching delivered by phone and secure text messaging. Results In a two-level linear mixed-effects model intention-to-treat analysis, significant between-group differences were found for the Beck Depression Inventory-II score (difference –8.54, P=.01), Quick Inventory of Depressive Symptoms score (difference –4.94, P=.001), Beck Anxiety Inventory score (difference –11.29, P<.001), and Brief Pain Inventory score (difference –1.99, P=.03), while marginal differences were found for the Five Facet Mindfulness Questionnaire–Nonjudging subscale (difference –2.68, P=.05). Conclusions These results confirm that youth depression can be effectively treated with online CBT-M that can be delivered with less geographic restriction. Trial Registration Clinical Trials.gov NCT03406052; https://www.clinicaltrials.gov/ct2/show/NCT03406052