This cohort study aims to examine the relationship between the occurrence of cranial nerve palsy (CNP) affecting the third, fourth, or sixth cranial nerve and the subsequent risk of stroke, with a particular focus on the modulating effect of age on this association. We established a cohort of individuals diagnosed with third, fourth, or sixth CNP who underwent national health screening within 2 years of diagnosis from 2010 to 2017. A control group was matched by sex and age at a ratio of 1:5. Participants were followed until December 31, 2019. We use multivariable Cox proportional hazards regression analyses to assess the association between ocular motor CNP and subsequent stroke stratified by age. Covariates including lifestyle, health behavior, underlying comorbidities, and Charlson comorbidity index score were also adjusted. Compared with the control group, the ocular motor CNP group had a higher risk of stroke after adjusting for potential confounders (hazard ratio [HR], 1.23 [95% CI,, 1.08-1.39]). The risk of stroke increased by 8.91 times in individuals with ocular motor CNP who were in their 30s (HR, 8.91 [95% CI, 1.63-48.66]). The risk increased by 2.49 times in those who were in their 40s, 1.78 times in those who were in their 50s, and 1.32 times in those who were in their 60s (HRs, 2.49, 1.78, and 1.32 [95% CI, 1.39-4.45, 1.31-2.42, and 1.08-1.62], respectively). However, for those who were in their 20s, 70s, or 80s, the incidence of stroke did not significantly increase. Our study establishes an association between ocular motor CNP and an increased risk of stroke, particularly in young adults.