John Stewart Waugh (April 25, 1929 – August 22, 2014) was an American chemist and Institute Professor at the Massachusetts Institute of Technology. He is known for developing average hamiltonian theory and using it to extend NMR spectroscopy, previously limited to liquids, to the solid state. He is the author of , a freeware general purpose Windows-based simulator of the spectra and dynamics of nuclear magnetic resonance (NMR). He has also used systems of a few coupled spins to illustrate the general requirements for equilibrium and ergodicity in isolated systems.