BACKGROUND: People living in rural Australia are more likely to die in hospital following an acute myocardial infarction than those living in major cities. While several factors, including time taken to access hospital care, contribute to this risk, it is also partially attributable to the lower uptake of evidence-based guidelines for the administration of thrombolytic drugs in rural emergency departments where up to one-third of eligible patients do not receive this life-saving intervention. Clinical pathways have the potential to link evidence to practice by integrating guidelines into local systems, but their impact has been hampered by variable implementation strategies and sub-optimal research designs. The purpose of this study is to determine the impact of a five-step clinical pathways implementation process on the timely and efficient administration of thrombolytic drugs for acute myocardial infarctions managed in rural Australian emergency departments. METHODS/DESIGN: The design is a two-arm, cluster-randomised trial with rural hospital emergency departments that treat and do not routinely transfer acute myocardial infarction patients. Six rural hospitals in the state of Victoria will participate, with three in the intervention group and three in the control group. Intervention hospitals will participate in a five-step clinical pathway implementation process: engagement of clinicians, pathway development according to local resources and systems, reminders, education, and audit and feedback. Hospitals in the control group will each receive a hard copy of Australian national guidelines for chest pain and acute myocardial infarction management. Each group will include 90 cases to give a power of 80% at 5% significance level for the two primary outcome measures: proportion of those eligible for thrombolysis receiving the drug and time to delivery of thrombolytic drug. DISCUSSION: Improved compliance with thrombolytic guidelines via clinical pathways will increase acute myocardial infarction survival rates in rural hospitals and thereby help to reduce rural-urban mortality inequalities. Such knowledge translation has the potential to be adapted for a range of clinical problems in a wide array of settings. TRIAL REGISTRATION: Australia New Zealand Clinical Trials Registry code ACTRN12608000209392.