The present disclosure pertains to a method and system configured to in-exsufflate a subject by controlling the in-exsufflation pressure waveform. In some embodiments, the system comprises a pressure generator, a subject interface, one or more sensors, one or more processors, electronic storage, a user interface, and/or other components. The system is configured to assist the subject to loosen and/or expel secretions by inducing a percussive pressure waveform delivered to the subject during inhalation and/or exhalation. The system is configured to control the in-exsufflation therapy delivered to the subject without requiring regular manual setting and/or adjustment of pressures, pressure amplitudes, a frequency range, and/or other parameters of the percussive pressure waveform.
