Objectives: The susceptibility of CT imaging to metallic objects gives rise to strong streak artefacts and skewed information about the attenuation medium around the metallic implants. This metal-induced artefact in CT images leads to inaccurate attenuation correction in PET/CT imaging. This study investigates the potential of deep learning-based metal artefact reduction (MAR) in quantitative PET/CT imaging. Methods: Deep learning-based metal artefact reduction approaches were implemented in the image (DLI-MAR) and projection (DLP-MAR) domains. The proposed algorithms were quantitatively compared to the normalized MAR (NMAR) method using simulated and clinical studies. Eighty metal-free CT images were employed for simulation of metal artefact as well as training and evaluation of the aforementioned MAR approaches. Thirty 18F-FDG PET/CT images affected by the presence of metallic implants were retrospectively employed for clinical assessment of the MAR techniques. Results: The evaluation of MAR techniques on the simulation dataset demonstrated the superior performance of the DLI-MAR approach (structural similarity (SSIM) = 0.95 ± 0.2 compared to 0.94 ± 0.2 and 0.93 ± 0.3 obtained using DLP-MAR and NMAR, respectively) in minimizing metal artefacts in CT images. The presence of metallic artefacts in CT images or PET attenuation correction maps led to quantitative bias, image artefacts and under- and overestimation of scatter correction of PET images. The DLI-MAR technique led to a quantitative PET bias of 1.3 ± 3% compared to 10.5 ± 6% without MAR and 3.2 ± 0.5% achieved by NMAR. Conclusion: The DLI-MAR technique was able to reduce the adverse effects of metal artefacts on PET images through the generation of accurate attenuation maps from corrupted CT images. Key points: • The presence of metallic objects, such as dental implants, gives rise to severe photon starvation, beam hardening and scattering, thus leading to adverse artefacts in reconstructed CT images. • The aim of this work is to develop and evaluate a deep learning-based MAR to improve CT-based attenuation and scatter correction in PET/CT imaging. • Deep learning-based MAR in the image (DLI-MAR) domain outperformed its counterpart implemented in the projection (DLP-MAR) domain. The DLI-MAR approach minimized the adverse impact of metal artefacts on whole-body PET images through generating accurate attenuation maps from corrupted CT images.