To compare the diameter of the jugular foramen (JF) between normal individuals and those with the diagnosis of craniovertebral junction abnormalities, such as Chiari malformation type I (CMI) and/or basilar invagination (BI). This cross-sectional analytical study measured the diameter of right and left JF in magnetic resonance imaging of patients that were split into four groups: 68 with combined CMI and BI (CMI+BI), 42 with isolated BI, 45 with isolated CMI, and 102 control cases. The t test determined sex differences, while univariate ANOVA with Tukey's post-hoc test assessed JF differences between groups. Considering all combinations of laterality and sex, CMI+BI had JF narrower than their respective controls. The JF was bilaterally narrower in BI than the control, only in females. Regardless of laterality, CMI had wider JF than the CMI+BI in males, and it did not differ from the control. In the females of CMI, the right JF did not differ from the control, and it was wider than the CMI+BI; while the left JF was narrower than the control, and it did not differ from the CMI+BI. JF narrowing is associated with CMI and BI when they are found combined in the same patient. When CMI or BI are detected separately, they do not imply evident changes in JF morphometry. It is expected that these findings could bring empiric substrate to support theories that claims a possible role of intracranial pressure disturbances as a triggering factor for CMI.