Tissue trauma associated with stent implantation continues to generate early thrombosis rates of 0.9% to 1.3% for both bare-metal and drug-eluting stent platforms. The Combo sirolimus-eluting stent combines an abluminal, bioabsorbable polymer with a luminal CD34+ antibody designed to capture endothelial progenitor cells. This article describes the design and methods of the HARMONEE trial (NCT02073565), which represents the first randomized controlled trial of the Combo design against a best-in-class contemporary everolimus-eluting stent. Up to 50 sites in Japan and the United States will enroll 286 subjects (271 evaluable) in each of 2 arms, for a total sample size of 572 subjects (542 evaluable). The statistical plan includes both superiority to imputed bare-metal stent control and noninferiority to everolimus-eluting stent on a primary clinical end point of target vessel failure at 1 year. In addition, fractional flow reserve assessment to evaluate the physiology of target vessels in the entire population will augment the end point definition of ischemia-driven target vessel revascularization. Finally, key safety considerations will be evaluated with a subpopulation with optical coherence tomography imaging for strut coverage, late strut malapposition, and plaque volume, as well as serial human antimurine antibody assessments. As the first international prospective randomized coronary intervention study under the “Harmonization by Doing” program, this study represents a unique collaboration between regulators and investigators in Japan and the United States.