Abstract Background Adolescence and young adulthood are critical times of initiation and progression to daily use of tobacco. However, it is difficult to recruit young adults to traditional smoking cessation and retention rates are typically low. Smartphone cessation applications (apps) can provide real-time responses to smoking urges and related cues, which are known to be important factors in lapse and relapse. Given the popularity of smartphones among young adults and the considerably higher download rates of commercially developed apps compared to research-based apps, there is a need to design pragmatic studies that evaluate commercial tobacco cessation apps. The aims of this pilot study are to assess the impact on tobacco cessation of using a smartphone app compared with usual care and to generate feasibility data to inform a future fully powered clinical trial. Methods We will conduct an open randomized controlled trial with parallel groups. Participants will be selected from hospitalized patients and must be aged 18–30 years, interested in cessation, smoked > 5 cigarettes/day over the past 30 days, and own an Apple or Android smartphone. Participants who are eligible will be randomized to either a smartphone experimental group or patient-initiated follow up (usual care). As this study seeks to assess feasibility, the primary data will include (1) recruitment rates, (2) retention rates, and (3) adherence, measured through user engagement with the app. Discussion This pilot trial will be the first to evaluate a commercially available smartphone app for tobacco cessation in a hospitalized setting. Data generated by this study can be used for larger fully powered trials such as comparative effectiveness studies against apps developed by academics or health scientists based on behavioral theories, or cost-effectiveness analyses of mobile interventions. Trial registration ClinicalTrials.gov, NCT03538678. Registered on 28 May 2018.