The thermal management and channel temperature evaluation of GaN power amplifiers are indispensable issues in engineering field. The transient thermal characteristics of pulse operated AlGaN/GaN high electron mobility transistors (HEMT) used in high power amplifiers are systematically investigated by using three-dimensional simulation with the finite element method. To improve the calculation accuracy, the nonlinear thermal conductivities and near-junction region of GaN chip are considered and treated appropriately in our numerical analysis. The periodic transient pulses temperature and temperature distribution are analyzed to estimate thermal response when GaN amplifiers are operating in pulsed mode with kilowatt-level power, and the relationships between channel temperatures and pulse width, gate structures, and power density of GaN device are analyzed. Results indicate that the maximal channel temperature and thermal impedance of device are considerably influenced by pulse width and power density effects, but the changes of gate fingers and gate width have no effect on channel temperature when the total gate width and active area are kept constant. Finally, the transient thermal response of GaN amplifier is measured using IR thermal photogrammetry, and the correctness and validation of the simulation model is verified. The study of transient simulation is demonstrated necessary for optimal designs of pulse-operated AlGaN/GaN HEMTs.