Heterogeneity of neointimal thickness is observed after drug-eluting stents implantation in bifurcation lesions (BL). We evaluated the vascular response of everolimus-eluting bioresorbable scaffold (BRS) struts deployed at BL using optical coherence tomography (OCT). 50 patients (64 scaffolds) underwent follow-up OCT after BRS implantation. Cross-sectional areas of each BL with a side branch more than 1.5 mm were analyzed using OCT every 200 µm. All images were divided into three regions according to shear stress: the 1/2 circumference of the vessel opposite to the ostium (OO), the vessel wall adjacent to the ostium (AO) and the side-branch ostium (SO). The %uncovered strut and the averaged neointimal thickness (NIT) were calculated. Overall, there were significant differences in both NIT and %uncovered strut among the three regions (OO, 119.2 ± 68.5 μm vs. AO, 94.2 ± 35.7 μm vs. SO, 80.5 ± 41.4 μm, p = 0.03; OO, 0.4 %vs. AO, 1.4 %vs. SO, 4.8 %, p = 0.02). Scaffolds were divided into two groups: a large-ratio side-branch group (LRSB; n = 32) and a small-ratio side-branch group (SRSB; n = 32), based on the median value of the ratio of the diameter of side branch ostium (Ds) to that of the main branch (Dm). In the LRSB alone, there were significant differences in both NIT and %uncovered strut among the three regions (OO, 128.0 ± 61.1 μm vs. AO, 97.3 ± 34.3 μm vs. SO, 75.9 ± 39.4 μm, p < 0.01; OO, 0.3 % vs. AO, 2.3 % vs. SO, 8.7 %, p < 0.01). After BRS implantation in BL, neointimal response was pronounced at the vessel wall opposite to the side branch ostium, especially in those with large side branches.