Objective: Long-term cost-effectiveness of app-based treatment for female stress, urgency, or mixed urinary incontinence (UI) compared to care-as-usual in primary care. Design: A pragmatic, randomised controlled, superiority trial. Setting: Primary care in the Netherlands from 2015 to 2018, follow-up at 12 months. Population: Women with ≥2 UI-episodes per week, access to mobile apps, wanting treatment. 262 women randomised equally to app or care-as-usual; 89 (68%) and 83 (63%) attended follow-up. Methods: The standalone app included conservative management for UI with motivation aids (e.g., reminders). Care-as-usual delivered according to the Dutch GP guideline for UI. Main outcome measures: Effectiveness assessed by the change in symptom severity score (ICIQ-UI-SF) and the change in quality of life (ICIQ-LUTS-QoL, EQ-5D-5L) on superiority with linear regression on an intention-to-treat basis. Cost-effectiveness and -utility from a societal perspective, based on Incontinence Impact Adjusted Life Years (IIALYs) and Quality Adjusted Life years (QALYs). Results: Clinically relevant improvement of UI severity for both app (-2.17 ± 2.81) and care-as-usual (-3.43 ± 3.6), with a non-significant mean difference of 0.903 (-0.66 to 1.871). Costs were lower for app-based treatment with \euro-161 (95%CI: -180 to -151) per year. Cost-effectiveness showed small mean differences in effect for IIALY (0.04) and QALY (-0.03) and thus larger ICER (-3,696) and ICUR (\euro6,379). Conclusion: App-based treatment is a viable alternative to care-as-usual for UI in primary care in terms of long-term cost-effectiveness. Funding: Dutch Organisation for Health Research and Development (ZonMw: 837001508), sub-funding P.W. Boer Foundation Dutch Trial Register identifier: Trial NL4948 (www.trialregister.nl/trial/4948).