Introduction Automated systems for ventilator management to date have been either fully heuristic rule-based systems or based on a combination of simple physiological models and rules. These have been shown to reduce the duration of mechanical ventilation in simple to wean patients. At present, there are no published studies that evaluate the effect of systems that use detailed physiological descriptions of the individual patient. The BEACON Caresystem is a model-based decision support system that uses mathematical models of patients’ physiology in combination with models of clinical preferences to provide advice on appropriate ventilator settings. An individual physiological description may be particularly advantageous in selecting the appropriate therapy for a complex, heterogeneous, intensive care unit (ICU) patient population. Methods and analysis Intenive Care weaning (iCareWean) is a single-blinded, multicentre, prospective randomised control trial evaluating management of mechanical ventilation as directed by the BEACON Caresystem compared with that of current care, in the general intensive care setting. The trial will enrol 274 participants across multiple London National Health Service ICUs. The trial will use a primary outcome of duration of mechanical ventilation until successful extubation. Ethics and dissemination Safety oversight will be under the direction of an independent committee of the study sponsor. Study approval was obtained from the regional ethics committee of the Health Research Authority (HRA), (Research Ethic Committee (REC) reference: 17/LO/0887. Integrated Research Application System (IRAS) reference: 226610. Results will be disseminated through international critical care conference/symposium and publication in peer-reviewed journal. Trial registration number ClinicalTrials.gov under NCT03249623 . This research is registered with the National Institute for Health Research under CPMS ID: 34831.