Objectives MRI can detect early-stage nasopharyngeal carcinoma (NPC), but the detection is more challenging in early-stage NPCs because they must be distinguished from benign hyperplasia in the nasopharynx. This study aimed to determine whether intravoxel incoherent motion diffusion-weighted imaging (IVIM DWI) MRI could distinguish between these two entities. Methods Thirty-four subjects with early-stage NPC and 30 subjects with benign hyperplasia prospectively underwent IVIM DWI. The mean pure diffusion coefficient ( D ), pseudo-diffusion coefficient ( D *), perfusion fraction ( f ) and apparent diffusion coefficient (ADC) values were calculated for all subjects and compared between the 2 groups using Student’s t test. Receiver operating characteristics with the area under the curve (AUC) was used to identify the optimal threshold for all significant parameters, and the corresponding diagnostic performance was calculated. A p value of < 0.05 was considered statistically significant. Results Compared with benign hyperplasia, early-stage NPC exhibited a significantly lower D mean (0.64 ± 0.06 vs 0.87 ± 0.11 × 10 −3  mm 2 /s), ADC 0–1000 mean (0.77 ± 0.08 vs 1.00 ± 0.13 × 10 −3  mm 2 /s), ADC 300–1000 (0.63 ± 0.05 vs 0.86 ± 0.10 × 10 −3  mm 2 /s) and a higher D * mean (32.66 ± 4.79 vs 21.96 ± 5.21 × 10 −3  mm 2 /s) (all p  < 0.001). No significant difference in the f mean was observed between the two groups ( p  = 0.216). The D and ADC 300–1000 mean had the highest AUC of 0.985 and 0.988, respectively, and the D mean of < 0.75 × 10 −3  mm 2 /s yielded the highest sensitivity, specificity and accuracy (100%, 93.3% and 96.9%, respectively) in distinguishing early-stage NPC from benign hyperplasia. Conclusion DWI has potential to distinguish early-stage NPC from benign hyperplasia and D and ADC 300–1000 mean were the most promising parameters. Key Points • Diffusion-weighted imaging has potential to distinguish early-stage nasopharyngeal carcinoma from benign hyperplasia in the nasopharynx. • The pure diffusion coefficient, pseudo-diffusion coefficient from intravoxel incoherent motion model and apparent diffusion coefficient from conventional diffusion-weighted imaging were significant parameters for distinguishing these two entities in the nasopharynx. • The pure diffusion coefficient, followed by apparent diffusion coefficient, may be the most promising parameters to be used in screening studies to help detect early-stage nasopharyngeal carcinoma.