Background: A drive to improve functional outcomes for patients undergoing total knee arthroplasty (TKA) has led to alternative alignment being used. Functional alignment (FA) uses intraoperative soft tissue tension to determine the optimal position of the prosthesis within the patient’s soft tissue envelope. Angular limits for bone resections are followed to prevent long-term prosthesis failure. This study will use the aid of robotic assistance to plan and implement the final prosthesis position. This method has yet to be compared to the traditional mechanically aligned (MA) knee in a randomised trial. Methods: A blinded randomised control trial with 100 patients will be undertaken via Perth Hip and Knee Clinic. Fifty patients will undergo a MA TKA and fifty will undergo a FA TKA. Both alignment techniques will be balanced via computer-assisted navigation to assess prosthetic gaps, being achieved via the initial bony resection and further soft tissue releases as required to achieve satisfactory balance. The primary outcome will be the Forgotten Joint Score (FJS) 2 years after surgery, with secondary outcomes being other patient-reported outcome measures, clinical functional assessment, radiographic position and complications. Other data that will be collected will be patient demography (sex, age, level of activity) and medical information (grade of knee injury, any other relevant medical information). The linear statistical model will be fitted to the response (FJS), including all the other variables as covariates. Discussion: Many surgeons are utilising alternative alignment techniques with a goal of achieving better functional outcomes for their patients. Currently, MA TKA remains the gold standard with good outcomes and excellent longevity. There is no published RCTs comparing FA to MA yet and only two registered studies are planned or currently in progress. This study utilises a FA technique which differs from the two studies. This study will help determine if FA TKA has superior functional results for patients. Trial registration: This trial has been registered with the Australian New Zealand Clinical Trials Registry (ANZCTR) http://www.anzctr.org.au: U1111-1257-2291, registered 25th Jan 2021. It is also listed on www.clinicaltrials.gov: NCT04748510.