AIMS: The Exercise Joins Education: Combined Therapy to Improve Outcomes in Newly-discharged Heart Failure (EJECTION-HF) study will evaluate the impact of a supervised exercise training programme (ETP) on clinical outcomes in recently hospitalized heart failure patients attending a disease management programme (DMP). Methods This multisite, pragmatic randomized controlled trial enrols patients discharged from participating hospitals with clinical evidence of heart failure who are willing and able to participate in a DMP and considered clinically safe to exercise. Enrolment includes participants with impaired and preserved left ventricular systolic function. Baseline assessment and programme commencement occur within 6 weeks of hospital discharge. The control group DMP includes individualized education and follow-up from a multidisciplinary heart failure team; a weekly education programme for 12 weeks; self-management advice; and medical follow-up. Home exercise is recommended for all participants. In addition, intervention participants are offered 36 supervised, structured gym-based 1 h exercise sessions over 24 weeks. Sessions are tailored to exercise capacity and include aerobic, resistance, and balance exercises. Enrolment target is 350 participants. Primary outcome is 12-month mortality and readmissions. Secondary outcomes include blinded evaluation of depressive symptoms, sleep quality, cognition, and functional status (activities of daily living, 6 min walk distance, grip strength) at 3 and 6 months. A cost-utility analysis will be conducted. CONCLUSION: This study will enrol a representative group of hospitalized heart failure patients and measure a range of patient and health service outcomes to inform the design of post-hospital DMPs for heart failure. Enrolment will be completed in 2013. ACTRN12608000263392.