Background Multiple sclerosis (MS) is a chronic disease of the central nervous system. As an association between MS and reduced cerebral venous blood drainage was hypothesised, our aim was to compare the size of the jugular foramina in patients with MS and in control subjects. Methods Ethics committee approval was received for this retrospective case–control study. We collected imaging and clinical data of 53 patients with MS (23 men, mean age 45 ± 9 years) and an age/gender-matched control group of 53 patients without MS (23 men, mean age 46 ± 10 years). The minimal diameter of both jugular foramina was measured on T1-weighted contrast-enhanced axial magnetic resonance images; the two diameters were summed. Student t test and Spearman correlation coefficient were used for analysis. Reproducibility was estimated using the Bland–Altman method. Results The mean diameter of the right foramen in patients with MS (6.3 ± 1.6 mm) was 10% smaller than that of the controls (7.0 ± 1.4 mm) ( p  = 0.020); the mean diameter of the left foramen in patients with MS (5.6 ± 1.3 mm) was 7% smaller than that of the controls (6.0 ± 1.3 mm) ( p  = 0.089). The sum of the diameters of both jugular foramina in patients with MS (mean 11.9 ± 2.3 mm) was 8% smaller ( p  = 0.009) than that of the controls (mean 13.0 ± 2.1 mm). The differences in diameters between patients with relapsing-remitting MS and patients with secondary progressive MS were not significant ( p  ≥ 0.332). There was no significant correlation between foramen diameters and the expanded disability status scale ( p  ≥ 0.079). Intra-reader and inter-reader reproducibility were 91% and 88%, respectively. Conclusions Jugular foramen diameter in patients with MS was 7-10% smaller than that in controls, regardless of the MS disease course.