BACKGROUND: Both pulmonary and mental health are affected following hospitalization for COVID-19 pneumonia. Pulmonary rehabilitation therapy has demonstrated benefits in improving mental health, but no validated combined programs that include mental health have been proposed. OBJECTIVE: This article presents the design of a trial that aimed to assess whether the participation in a combined rehabilitation program that includes home-based respiratory physiotherapy and telephone-based psychological support is associated with a greater improvement of pulmonary and mental health outcomes 7-12 weeks after COVID-19 hospitalization discharge compared with posthospital usual care provided by a public Peruvian hospital. METHODS: WAYRA (the word for air in the Quechua language) was an open-label, unblinded, two-arm randomized controlled trial. We recruited 108 participants aged 18-75 years who were discharged from the hospital after COVID-19 pneumonia that required >6 liters/minute of supplemental oxygen during treatment. Participants were randomly assigned at a 1:1 ratio to receive the combined rehabilitation program or usual posthospital care provided by a public Peruvian hospital. The intervention consisted of 12 at-home respiratory rehabilitation sessions and 6 telephone-based psychological sessions. The primary outcome was the 6-minute walk distance. Secondary outcomes included lung function, mental health status (depression, anxiety, and trauma), and quality of life. Outcomes were assessed at baseline (before randomization) and at 7 and 12 weeks after hospital discharge to assess the difference between arms. RESULTS: This study was funded by the Peruvian National Council of Science Technology and Technology Innovation in July 2020. Ethics approval was obtained on September 2, 2020. Recruitment and data collection occurred between October 2020 and June 2021. Results are expected to be published by the end of 2022. CONCLUSIONS: WAYRA was the first randomized controlled trial evaluating combined pulmonary-mental health rehabilitation for hospitalized COVID-19 survivors in resource-limited settings, potentially providing a foundation for the cost-effective scale-up of similar multidisciplinary rehabilitation programs. TRIAL REGISTRATION: ClinicalTrials.gov NCT04649736; https://clinicaltrials.gov/ct2/show/NCT04649736. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/36001.