Aim: We focused on the ratios of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) to arachidonic acid (AA) and explored the significance of these ratios relative to clinical characteristics by age in ischemic stroke patients.Methods: We enrolled patients with acute ischemic stroke who underwent radiological investigations and laboratory examinations, including measurement of serum EPA, DHA, and AA levels, and controls. Patients were classified according to age (< 65, 65–74, and ≥ 75 years) and the tertile of EPA/AA and DHA/AA ratios, and clinical aspects were compared with these factors.Results: We analyzed 373 patients (age 70.2 ± 13.4 years; 245 males) and 105 controls. Among stroke patients, patients aged < 65 years had the lowest EPA/AA (0.35 ± 0.23, p = 0.006) and DHA/AA (0.73 ± 0.27, p < 0.001) ratios. Compared with controls, patients aged < 65 years showed lower EPA/AA (vs. 0.49 ± 0.25, p < 0.001) and DHA/AA (vs. 0.82 ± 0.26, p = 0.009) ratios. From logistic regression analysis, the EPA/AA (odds ratio 0.18, 95% confidence interval 0.04–0.81, p = 0.026) and DHA/AA (odds ratio 0.09, 95% confidence interval 0.02–0.33, p < 0.001) ratios were inversely related to patients aged < 65 years. According to age-stratified analyses, we found an association of aortic arch calcification with a lower EPA/AA ratio for patients aged ≥ 75 years and an association of multiple infarctions and cerebral white matter lesions with a lower EPA/AA ratio for patients aged 65–74 years (p < 0.05).Conclusions: The ratios of EPA/AA and DHA/AA could be specific markers for younger stroke patients. The EPA/AA ratio may be related to aortic arch calcification for elderly stroke patients and to multiple infarctions and cerebral white matter disease for middle-aged stroke patients.