Ellis was elected a Fellow of the American Physical Society in 1988 and a Fellow of the Royal Society of London in 2009. Also in 2009, Ellis together with John Collins and Davison Soper won the J. J. Sakurai Prize for Theoretical Particle Physics, For work in perturbative Quantum Chromodynamics, including applications to problems pivotal to the interpretation of high energy particle collisions. In 2019 he was awarded the Paul Dirac Medal of the Institute of Physics, For his seminal work in quantum chromodynamics (QCD) where he performed many of the key calculations that led to the acceptance of QCD as the correct theory of the strong interaction.