A low ratio of eicosapentaenoic acid to arachidonic acid (EPA/AA) has been demonstrated to be associated with a higher risk of cardiovascular events. Optical coherence tomography (OCT) is useful for the assessment of coronary plaque vulnerability. The purpose of this study was to evaluate the association between EPA/AA ratio and coronary plaque vulnerability. This study involved 58 patients with stable angina pectoris undergoing percutaneous coronary intervention. OCT image acquisition was performed before the procedure in the culprit lesions. We assessed lipid-rich plaque length and arc, fibrous cap thickness, frequency of thin-cap fibroatheroma (TCFA), thrombus, ruptured plaque, macrophage infiltration, and microvessels using OCT. Patients were divided into two groups according to the median value of serum EPA/AA ratio: a low-EPA/AA group (n = 29, EPA/AA ratio <0.36) and a high-EPA/AA group (n = 29, EPA/AA ratio ≥0.36). In qualitative analyses, TCFA (35.4 vs 6.9 %, P = 0.0095), macrophage infiltration (48.3 vs 13.8 %, P = 0.0045), and microvessels (44.8 vs 10.3 %, P = 0.0033) were more frequently observed in the low-EPA/AA group. In quantitative analyses, the low-EPA/AA group had wider maximum lipid arc (114.0 ± 94.8° vs 56.4 ± 66.0°, P = 0.0097), longer lipid length (4.8 ± 4.5 vs 1.6 ± 2.6 mm, P = 0.0037), and thinner fibrous cap (69.3 ± 28.3 vs 113.3 ± 46.6 μm, P = 0.005) compared with the high-EPA/AA group. EPA/AA ratio was positively correlated with fibrous cap thickness (r = 0.46, P = 0.007). In a multivariate model, an EPA/AA ratio <0.36 was associated with the presence of TCFA (odds ratio 6.41, 95 % confidence interval 1.11–61.91, P = 0.0371). In our detailed OCT analysis, lower EPA/AA ratio was associated with higher vulnerability of coronary plaques to rupture.