This report summarizes the contributions presented at the 16th IAEA Technical Meeting on Energetic Particles in Magnetic Confinement Systems—Theory of Plasma Instabilities, held in Shizuoka, Japan, 3–6 September 2019. The meeting brought together about 100 experts from nuclear fusion research sites worldwide to discuss the physics of energetic particles and plasma instabilities, at the first joint meeting from the two scientific disciplines. The main topics of the meeting were: alpha particles physics; transport of energetic particles; effects of energetic particles in magnetic confinement fusion devices; collective phenomena such as Alfvén eigenmodes, energetic particle modes and others; runaway electrons and disruptions; diagnostics for energetic particles; control of energetic particles confinement; multiscale physics and instabilities in burning plasmas.