Introduction. Initiation of acute kidney replacement therapy (KRT) is common in critically ill adults admitted to the intensive care unit (ICU), and is associated with increased morbidity and mortality. KRT has been linked to poor neurocognitive outcomes, leading to a reduced quality of life, as well as increased utilization of healthcare resources. Adults initiated on dialysis in the ICU may be particularly at risk of neurocognitive impairment, as survivors of critical illness are already predisposed to developing cerebrovascular disease and cognitive dysfunction over the long-term relative to healthy controls. Regional cerebral oxygen saturation (rSO2) may provide a critical early marker of long-term neurocognitive impairment in patients in this population. The INCOGNITO-AKI study aims to understand cerebral oxygenation in patients undergoing KRT, either continuous or intermittent, in the ICU. These findings will be correlated with long-term cognitive and functional outcomes, as well as structural brain pathology. Methods and analysis. 108 patients scheduled to undergo treatment for acute kidney injury with KRT in the Kingston Health Sciences Centre ICU will be recruited into this prospective observational study. Enrolled patients will be assessed with intradialytic cerebral oximetry using near infrared spectroscopy (NIRS). Delirium will be assessed daily with the Confusion Assessment Method-Intensive Care Unit (CAM-ICU) and delirium severity quantified as cumulative CAM-ICU-7 scores. Neurocognitive impairment will be assessed at 3- and 12-months after hospital discharge using the Kinarm and Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). Structural brain pathology on MRI will also be measured at the same timepoints. Driving safety, adverse events, and medication adherence will be assessed at 12-months to evaluate the impact of neurocognitive impairment on functional outcomes. Ethics and dissemination. This study has been approved by the Queen's University Health Sciences and Affiliated Teaching Hospitals Research Ethics Board (Approval number: DMED-2424-20). Results will be presented at critical care scientific conferences and a lay summary will be provided to patients and families in their preferred format.