BACKGROUND: The RATE trial is a three-arm non-inferiority randomized controlled trial in adult patients treated with extracorporeal membrane oxygenation (ECMO) on the effect of anticoagulation levels on mortality, hemorrhagic, and thrombotic complications. The current protocol presents the rationale and analysis plan for evaluating the primary and secondary outcomes under the Bayesian framework. METHODS: This protocol was drafted and submitted before study completion and, thus, the primary analysis. The primary outcome of the Bayesian analysis is mortality at 6 months. The secondary outcomes are severe hemorrhagic and thrombotic complications. We will use an uninformative prior for the primary analysis. Sensitivity analyses will be performed using a skeptical prior and an evidence-based informative prior. CONCLUSION: The proposed secondary, pre-planned Bayesian analysis of the RATE trial will provide additional information on the effect of different anticoagulation strategies during ECMO on complication rates. This additional Bayesian analysis will likely increase the validity of our results and complement the interpretation of the primary and several secondary outcomes. TRIAL REGISTRATION: This trial is registered at https://clinicaltrials.gov/ (NCT04536272), registration date September 2, 2020. This trial is also registered at the Dutch trial register (NL7976).