This study aimed to estimate the additional dose the cone-beam computed tomography (CBCT) system integrated into the Varian TrueBeam linear accelerator delivers to a patient with head and neck cancer using mesh-type International Commission on Radiological Protection (ICRP) Reference Computational Phantoms. In the first part, for use as a benchmark for the accuracy of the Monte Carlo geometry of CBCT, Particle and Heavy Ion Transport code System (PHITS) calculations were confirmed against measured lateral and depth dose profiles using a CT dose profiler (CTDP). After obtaining good agreement, organ dose calculations were performed by PHITS using mesh-type reference computational phantom (MRCP) and irradiating the neck region; the effective dose was calculated utilising absorbed organ doses and tissue weighting factors for male and female MRCP. Substantially, it has been found that the effective doses for male and female MRCP are 0.81 and 1.06 mSv, respectively. As this study aimed to assess the imaging dose from the CBCT system used in image-guided radiation therapy (IGRT), it is required to take into account this dose in terms of both the target organ and surrounding tissues. Although the absorbed organ dose values and effective dose values obtained for both MRCP males and females were small, attention should be paid to the additional dose resulting from CBCT. This study can create awareness on the importance of doses arising from imaging techniques, especially CBCT.