BackgroundPatellofemoral pain (PFP) is a common knee disorder that causes persistent pain, lower self-reported function and quality of life. People with PFP also present with altered psychological factors, which are associated with higher levels of pain and dysfunction. Mindfulness-based interventions (MBI) generally consist of meditative practices developed to provide a holistic approach to chronic conditions. However, the effects of MBI on clinical and psychological outcomes for people with PFP remains understudied.MethodsThis assessor-blinded, parallel, two-arm randomized clinical trial aims to investigate the effects of adding an 8-week online MBI program to exercise therapy and patient education on clinical and psychological factors for people with PFP. We also aim to investigate whether psychological factors mediate changes in pain and function. Sixty-two participants with PFP will be recruited and randomized into one of two treatment groups (Mindfulness or Control group). Both groups will receive an 8-week intervention involving exercise therapy and education delivered through an online platform. The Mindfulness group will additionally receive a MBI component including formal and informal practices. Outcomes will be assessed online at baseline, intervention endpoint (follow-up 1) and 12 months after intervention completion (follow-up 2). Comparisons between groups will be performed at all time points with linear mixed models. A mediation analysis will be performed using a 3-variable framework.DiscussionExercise therapy and patient education are considered the “best management” options for PFP. However, unsatisfactory long-term prognosis remains an issue. It is known that people with PFP present with altered psychological factors, which should be considered during the evaluation and treatment of people with PFP. Adding a MBI to the current best treatment for PFP may improve short and long-term effects by addressing the underlying psychological factors.Trial registrationRegistro Brasileiro de Ensaios Clínicos(ReBEC) RBR-4yhbqwk, registered in April 6, 2021.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12891-023-06491-x.