Purpose Convolutional neural networks (CNNs) show potential for delineating cancers on contrast-enhanced MRI (ce-MRI) but there are clinical scenarios in which administration of contrast is not desirable. We investigated performance of the CNN for delineating primary nasopharyngeal carcinoma (NPC) on non-contrast-enhanced images and compared the performance to that on ce-MRI. Materials and methods We retrospectively analyzed primary NPC in 195 patients using a well-established CNN, U-Net, for tumor delineation on the non-contrast-enhanced fat-suppressed (fs)-T2W, ce-T1W and ce-fs-T1W images. The CNN-derived delineations were compared to manual delineations to obtain Dice similarity coefficient (DSC) and average surface distance (ASD). The DSC and ASD on fs-T2W were compared to those on ce-MRI. Primary tumor volumes (PTVs) of CNN-derived delineations were compared to that of manual delineations. Results The CNN for NPC delineation on fs-T2W images showed similar DSC (0.71 ± 0.09) and ASD (0.21 ± 0.48 cm) to those on ce-T1W images (0.71 ± 0.09 and 0.17 ± 0.19 cm, respectively) ( p  > 0.05), and lower DSC but similar ASD to ce-fs-T1W images (0.73 ± 0.09, p  < 0.001; and 0.17 ± 0.20 cm, p  > 0.05). The CNN overestimated PTVs on all sequences ( p  < 0.001). Conclusion The CNN showed promise for NPC delineation on fs-T2W images in cases where it is desirable to avoid contrast agent injection. The CNN overestimated PTVs on all sequences.