Abstract Background Mid-portion Achilles tendinopathy is a common musculoskeletal condition characterised by degeneration of the Achilles tendon, which causes pain and disability. Multiple non-surgical treatments have been advocated for this condition including calf muscle eccentric exercise and in-shoe heel lifts. Although adherence is challenging, there is evidence to suggest that calf muscle eccentric exercise is effective in decreasing pain and improving function in people with Achilles tendinopathy. Heel lifts reduce ankle joint dorsiflexion and Achilles tendon strain, however their efficacy in the management of Achilles tendinopathy is unclear. This article describes the design of a parallel-group randomised trial comparing the efficacy of heel lifts to calf muscle eccentric exercise for Achilles tendinopathy. Methods Ninety-two participants with Achilles tendinopathy will be randomised to one of two groups: (i) a heel lift group that will receive pre-fabricated 12 mm in-shoe heel lifts (Clearly Adjustable®), or (ii) an exercise group that will be advised to carry out a calf muscle eccentric exercise program (twice a day, 7 days a week, for 12 weeks). Outcome measures will be obtained at baseline, 2, 6 and 12 weeks; the primary endpoint for assessing efficacy being 12 weeks. The primary outcome measure will be the total score of the Victorian Institute of Sport Assessment – Achilles (VISA–A) questionnaire. Secondary outcome measures will include thickness and integrity of the Achilles tendon (using ultrasound tissue characterisation [UTC]), participant perception of treatment effect on pain and function (using the 7-point Patient Global Impression of Change scale), severity of pain at the Achilles tendon (using a 100 mm visual analogue scale) in the previous week, health status (using the EuroQol-5D-5L™ questionnaire), physical activity levels (using the 7-day Recall Physical Activity Questionnaire) and calf muscle function (using the standing heel rise test). Data will be analysed using the intention to treat principle. Discussion The HEALTHY trial (Heel lifts versus calf muscle eccentric Exercise for AchiLles TendinopatHY) is the first randomised trial to compare the efficacy of heel lifts to calf muscle eccentric exercise in reducing pain and improving function in people with Achilles tendinopathy. A pragmatically designed trial was developed to ensure that if the interventions are found to be effective, the findings can be readily implemented in clinical practice. Trial registration Australian New Zealand Clinical Trials Registry: ACTRN12617001225303. Registered on August 22nd, 2017.