BackgroundPersistent knee pain in people over 50 years of age is often attributable to knee osteoarthritis (OA), a common joint condition that causes physical and psychological dysfunction. Exercise and pain coping skills training (PCST) can help reduce the impact of persistent knee pain, however, access to health professionals who deliver these services can be challenging. With increasing access to the Internet, remotely delivered Internet-based treatment approaches may provide alternatives for healthcare delivery. This pragmatic randomised controlled trial will investigate whether an Internet-delivered intervention that combines PCST and physiotherapist-guided exercise (PCST + Ex) is more effective than online educational material (educational control) in people with persistent knee pain.Methods/DesignWe will recruit 148 people over 50 years of age with self-reported persistent knee pain consistent with knee OA from the Australian community. Following completion of baseline questionnaires, participants will be randomly allocated to access a 3-month intervention of either (i) online educational material, or (ii) the same online material plus an 8-module (once per week) Internet-based PCST program and seven Internet-delivered physiotherapy sessions with a home exercise programs to be performed 3 times per week. Outcomes will be measured at baseline, 3 months and 9 months with the primary time point at 3 months. Primary outcomes are average knee pain on walking (11-point numeric rating scale) and self-reported physical function (Western Ontario and McMaster Universities Osteoarthritis Index subscale). Secondary outcomes include additional measures of knee pain, health-related quality-of-life, perceived global change in symptoms, and potential moderators and mediators of outcomes including self-efficacy for pain management and function, pain coping attempts and pain catastrophising. Other measures of adherence, adverse events, harms, use of health services/co-interventions, and process measures including appropriateness and satisfaction of the intervention, will be collected at 3, 6 and 9 months.DiscussionThe findings will help determine the effectiveness and acceptability of Internet access to a combination of interventions that are known to be beneficial to people with persistent knee pain. This study has the potential to guide clinical practice towards innovative modes of healthcare provision.Trial registrationAustralian New Zealand Clinical Trials Registry reference: ACTRN12614000243617.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2474-15-279) contains supplementary material, which is available to authorized users.