The aim of this study was to investigate the association between ocular motor cranial nerve palsies (OMCNP) and the occurrence of primary malignant brain tumors in a Korean population, using the national sample cohort database from Korea National Health Insurance Service (KNHIS). KNHIS data between 2010 and 2017 were analyzed. Our sample encompassed 118,686 participants, including 19,781 from a recently diagnosed OMCNP cohort and 98,905 from a matched control cohort through a 1:5 propensity score matching based on age and gender. To counteract the issue of reverse causation, we integrated a one-year time lag in our sensitivity analysis. Study participants were followed up until 31 December 2019. Cox proportional hazard regression analysis was used to compute the adjusted hazard ratio (HR) for primary malignant brain tumors according to the OMCNP diagnosis. Additionally, we performed a subgroup analysis to discern effects of various factors on the association between OMCNP and primary malignant brain tumors. HR for primary malignant brain tumors was 3.272 (95% confidence interval [CI]: 2.294 to 4.665) in the OMCNP cohort compared to the control cohort in a fully adjusted model for age, sex, socio-economic status, smoking, drinking, regular physical exercise, hypertension, diabetes, dyslipidemia, obesity, chronic kidney disease, and human immunodeficiency virus infection. Further subgroup analysis revealed that the risk of primary malignant brain tumors was significantly increased in women with OMCNP compared to men with OMCNP (HR: 5.118 in women vs. 2.441 in men, p = 0.0440), and in those aged <65 years than in those aged ≥65 years (HR: 6.951 in age < 65 years vs. 1.899 in age ≥ 65 years, p = 0.0006). Our population-based cohort study demonstrated a significantly increased risk of subsequent primary malignant brain tumors in patients with OMCNP. Particularly, OMCNP-afflicted women aged below 65 manifested a heightened probability of developing primary malignant brain tumors compared to those devoid of OMCNP.