BACKGROUND: Mental health problems among workers cause enormous losses to companies in Japan. However, workers have been considered to have limited access to psychological support because of time constraints, which makes it difficult for them to engage in face-to-face psychological support interventions. OBJECTIVE: This study aimed to present an intervention protocol that describes a randomized controlled trial to examine whether brief guided mindfulness meditation (MM) or self-compassion meditation (SCM) provided by a smartphone app is effective for mental health and work-related outcomes among workers. METHODS: This is an open-label, 3-arm randomized controlled trial. The participants will be recruited through an open call on relevant websites with the following inclusion criteria: (1) employees who are working more than 20 hours per week, (2) between the ages of 18 and 54 years, (3) not on a leave of absence, (4) not business owners or students, and (5) not currently diagnosed with a mental disorder and have a Kessler Psychological Distress Scale-6 score below 13 points. We will include 200 participants and randomly assign them to an SCM course (n=67), an MM course (n=67), and a waitlist group (n=66). The intervention groups (SCM and MM) will be instructed to engage in daily guided self-help, self-compassion, and MMs lasting 6-12 minutes per day over 4 weeks. Primary outcomes will include psychological distress and job performance, and secondary outcomes will include somatic symptoms, cognitive flexibility, self-esteem, self-compassion, perceived stress, well-being, emotion regulation, work engagement, anger, psychological safety, and creativity. All procedures were approved by the ethics committee of the University of Tokyo (22-326). All participants will be informed of the study via the websites, and written informed consent will be collected via web-based forms. RESULTS: The recruitment of participants began in December 2022, and the intervention began in January 2023. As of September 2023, a total of 375 participants have been enrolled. The intervention and data collection were completed in late October 2023. CONCLUSIONS: This study will contribute to the development of effective self-care intervention content that will improve mental health, work performance, and related outcomes and promote mindful and self-compassionate attitudes when faced with distress. TRIAL REGISTRATION: University Hospital Medical Information Network Clinical Trials Registry UMIN000049466; https://tinyurl.com/23x8m8nf. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/53541.