Retraining programs in vocational rehabilitation are often characterized by a low level of physical activity, even when targeting jobs with primarily physical demands. They might therefore be accompanied by a decline in functional capacity if the lack of physical activity is not compensated by increased activity during leisure time. The implementation of a work-related exercise app might be a promising approach to promoting a return to work in vocational rehabilitation. We developed the "WORKout-app" which provides exercise plans based on a comparison of the physical demands of the retraining profession and the current functional capacity. The aim of this study is to examine the effects of app-based exercise during vocational rehabilitation on perceived work ability (primary outcome), occupational self-efficacy, days of sick leave, and return to work (secondary outcomes). We conducted a cluster-randomized controlled trial with 2 arms (intervention: WORKout-app vs control: treatment as usual) in 4 cohorts of 5 vocational rehabilitation centers in Germany. Participants are nested within retraining classes per vocational rehabilitation center and per cohort assigned to either the intervention condition or the control condition. The target sample size at the participant level is 598. Measurement time points include baseline, the end of rehabilitation, 3 months after the end of rehabilitation, and 6 months after the end of rehabilitation. Linear and generalized linear mixed-effects models are performed to test for treatment differences in outcomes. This study is funded by the German Federal Pension Insurance. The trial is registered with the German Clinical Trials Register (DRKS00030775) and approved by the Ethics Committee of the German Sport University Cologne (145/2022). The findings of the study will inform researchers and practitioners about the effectiveness of an exercise app developed to counteract the effects of physical inactivity during vocational rehabilitation. DERR1-10.2196/50200.