This study aimed to determine the feasibility and limitations of deep learning-based coronary calcium scoring using positron emission tomography-computed tomography (PET-CT) in comparison with coronary calcium scoring using ECG-gated non-contrast-enhanced cardiac computed tomography (CaCT). A total of 215 individuals who underwent both CaCT and PET-CT were enrolled in this retrospective study. The Agatston method was used to calculate the coronary artery calcium scores (CACS) from CaCT, PET-CT(reader), and PET-CT(AI) to analyse the effect of using different modalities and AI-based software on CACS measurement. The total CACS and CACS classified according to the CAC-DRS guidelines were compared between the three sets of CACS. The differences, correlation coefficients, intraclass coefficients (ICC), and concordance rates were analysed. Statistical significance was set at p < 0.05. The correlation coefficient of the total CACS from CaCT and PET-CT(reader) was 0.837, PET-CT(reader) and PET-CT(AI) was 0.894, and CaCT and PET-CT(AI) was 0.768. The ICC of CACS from CaCT and PET-CT(reader) was 0.911, PET-CT(reader) and PET-CT(AI) was 0.958, and CaCT and PET-CT(AI) was 0.842. The concordance rate between CaCT and PET-CT(AI) was 73.8%, with a false-negative rate of 37.3% and a false-positive rate of 4.4%. Age and male sex were associated with an increased misclassification rate. Artificial intelligence-assisted CACS measurements in PET-CT showed comparable results to CACS in coronary calcium CT. However, the relatively high false-negative results and tendency to underestimate should be of concern. Application of automated calcium scoring to PET-CT studies could potentially select patients at high risk of coronary artery disease from among cancer patients known to be susceptible to coronary artery disease and undergoing routine PET-CT scans. • Cancer patients are susceptible to coronary disease, and PET-CT could be potentially used to calculate coronary artery calcium score (CACS). • Calcium scoring using artificial intelligence in PET-CT automatically provides CACS with high ICC to CACS in coronary calcium CT. • However, underestimation and false negatives of CACS calculation in PET-CT should be considered.