An in-vehicle noise control system is provided. The system includes speakers that output navigation guidance sound and audio content reproduced at a head unit of a vehicle. An audio module receives the navigation guidance sound and an audio content signal to generate an opposite waveform with respect to the navigation guidance sound and output noise offset waveforms in which tuning functions are calculated based on positions of the speakers to the opposite waveform. An amplifier is connected between the audio module and the speakers. The audio module outputs the navigation guidance sound and the audio content signal to one of the speakers located at a driver's seat and outputs the noise offset waveforms and the audio content signal to the remaining speakers.