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: We developed a combined home-based respiratory physiotherapy and telephone-based psychological support intervention aimed at improving pulmonary and mental health outcomes 7-12 weeks after COVID-19 hospitalization discharge. Here we present the design and methodology of the trial. Methods: WAYRA (air in Quechua) was an open-label, unblinded, two-arm feasibility randomized controlled trial. We recruited 108 participants aged 18–75 years who were discharged from the hospital after COVID-19 pneumonia that required >6 L/min of supplemental oxygen during treatment. Participants were randomly assigned to receive the intervention or usual care in a 1:1 ratio. The intervention consisted of twelve at-home respiratory rehabilitation sessions and six telephone-based structured psychological sessions. The primary outcome was the six-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. Results: Recruitment and data collection occurred between October 2020 and June 2021 (ethics approval was obtained on September 02, 2020). A total of 103 participants completed the baseline assessments. Analyses of sample characteristics, primary and secondary outcomes are currently underway, with results expected to be published by the end of 2022. Conclusions: WAYRA aims to be 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 scaling-up of similar multidisciplinary rehabilitation programs. Clinical Trial: ClinicalTrials.gov,ID:NCT04649736