This study evaluated the impact of contrast material (CM) on radiation dose for adults undergoing computed tomography pulmonary angiography (CTPA). A previously developed physiologically based pharmacokinetic (PBPK) model and phantoms representing the average (reference) adult male and female individual were used to evaluate the iodine concentration in tissues as a function of time elapsed since the initiation of iodinated contrast medium administration. In order to estimate the radiation dose more accurately, a detailed model of pulmonary vessels was added to the phantoms. Then, the material composition of phantoms was modified to include the iodine concentration in different organs and tissues at different acquisition times after CM injection. The calculations were performed using Monte Carlo N-Particle extended code (MCNPX) version 2.6.0.The radiation dose estimates during CTPA were provided as a function of scan acquisition time after injection considering the distribution of iodinated CM within ICRP reference phantoms. It was shown that the estimated radiation dose to the lungs could be 31–40% (27–34%) larger when considering the effect of iodinated contrast administration with injection rate of 5 (3)mL/s. Moreover, the effective dose for contrast-enhanced CT (CECT) would be utmost 10–13% larger than that for non-enhanced CT (NECT). The radiation doses to the other organs in-/outside the scanned region would be decreased if the scan performed on time. In case of late scanning, absorbed dose decreases slightly for lungs (∼15–20%) whereas becomes (∼10% or more) higher than its NECT value for some organs such as heart muscle, kidneys, and spleen. To sum up, the late scanning (Δt>5s after the end of injection) is not recommended because of higher dose delivered to other organs than the lungs (particularly heart muscle).