Methods for RF pulse reflection reduction are provided herein. In some embodiments, a method for processing a substrate in a plasma enhanced substrate processing system using multi-level pulsed RF power includes; receiving a process recipe for processing the substrate that includes a plurality of pulsed RF power waveforms from a plurality of RF generators, using the master RF generator to generate a transistor-transistor logic (TTL) signal having a base frequency and a first duty cycle, setting a multiplier for each RF generator, dividing the first duty cycle into a high level interval and a low level interval, determining a frequency command set for each RF generator and sending the frequency command set to each RF generator, wherein the frequency command set includes a frequency set point for each RF generator; and providing the plurality of pulsed RF power waveforms from the plurality of RF generators to a process chamber.