Background: Midportion Achilles tendinopathy (AT) is a common overuse injury, usually requiring several months of rehabilitation. Exercise therapy of the ankle plantar flexors (i.e. tendon loading) is considered crucial during conservative rehabilitation. Alfredson's isolated eccentric and Silbernagel's combined concentric-eccentric exercise programs have both shown beneficial results, but it is unknown whether any of these programs is superior for use in clinical practice. Therefore, the primary objective of this study is to compare the effectiveness of both programs on clinical symptoms. Secondary objectives are to compare the effectiveness of both programs on quality of life and functional outcome measures, to investigate the prognostic value of baseline characteristics, to investigate differences in cost-effectiveness. Methods/Design: Eighty-six recreational athletes (21-60 years of age) with unilateral chronic midportion AT (i.e. ≥ 3 months) will be included in this multicenter assessor blinded randomized controlled trial. They will be randomly allocated to either a group performing the Alfredson isolated eccentric training program (n = 43), or a group performing the Silbernagel combined concentric-eccentric program (n = 43). In the Alfredson group, participants will perform eccentric heel-drops on their injured side, twice daily for 12 weeks, whereas in the Silbernagel group, participants perform various concentric-eccentric heel-raise exercises, once daily for 12 weeks. Primary outcome measure will be the Victorian Institute of Sport Assessment - Achilles (VISA-A) questionnaire. Secondary outcomes will be a visual analogue scale (VAS) for pain during daily activities and sports, duration of morning stiffness, global perceived effect, the 12-item Short Form Health Survey and the Euroqol instrument, and functional performance measured with the heel-raise test and the countermovement jump. Additionally, alongside the RCT, a cost-effectiveness analysis will be performed. Assessments will be performed at baseline and after 12, 26, and 52 weeks. Discussion: This study is the first to directly compare the Alfredson and the Silbernagel exercise program in a randomized trial. The results can further enlarge the evidence base for choosing the most appropriate exercise program for patients with midportion AT. Trial registration: Dutch Trial register: NTR5638. Date of registration: 7 January 2016