Background: Psychological interventions for the prevention of depression might be a cost-effective way to reduce the burden associated with depressive disorders. Objective: To evaluate the cost-effectiveness of a Web-based guided self-help intervention to prevent major depressive disorder (MDD) in people with subthreshold depression (sD). Methods: A pragmatic randomized controlled trial was conducted with follow-up at 12 months. Participants were recruited from the general population via a large statutory health insurance company and an open access website. Participants were randomized to a Web-based guided self-help intervention (ie, cognitive-behavioral therapy and problem-solving therapy assisted by supervised graduate students or health care professionals) in addition to usual care or to usual care supplemented with Web-based psycho-education (enhanced usual care). Depression-free years (DFYs) were assessed by blinded diagnostic raters using the telephone-administered Structured Clinical Interview for DSM-IV Axis Disorders at 6- and 12-month follow-up, covering the period to the previous assessment. Costs were self-assessed through a questionnaire. Costs measured from a societal and health care perspective were related to DFYs and quality-adjusted life years (QALYs). Results: In total, 406 participants were enrolled in the trial. The mean treatment duration was 5.84 (SD 4.37) weeks. On average, participants completed 4.93 of 6 sessions. Significantly more DFYs were gained in the intervention group (0.82 vs 0.70). Likewise, QALY health gains were in favor of the intervention, but only statistically significant when measured with the more sensitive SF-6D. The incremental per-participant costs were €136 (£116). Taking the health care perspective and assuming a willingness-to-pay of €20,000 (£17,000), the intervention's likelihood of being cost-effective was 99% for gaining a DFY and 64% or 99% for gaining an EQ-5D or a SF-6D QALY. Conclusions: Our study supports guidelines recommending Web-based treatment for sD and adds that this not only restores health in people with sD, but additionally reduces the risk of developing a MDD. Offering the intervention has an acceptable likelihood of being more cost-effective than enhanced usual care and could therefore reach community members on a wider scale. Trial registration: German Clinical Trials Register: DRKS00004709; http://www.drks.de/DRKS00004709 (Archived by WebCite at http://www.webcitation.org/6kAZVUxy9).