Optical coherence tomography based computational flow dynamic (CFD) modeling provides detailed information about the local flow behavior in stented/scaffolded vessel segments. Our aim is to investigate the in-vivo effect of strut thickness and strut protrusion on endothelial wall shear stress (ESS) distribution in ArterioSorb Absorbable Drug-Eluting Scaffold (ArterioSorb) and Absorb everolimus-eluting Bioresorbable Vascular Scaffold (Absorb) devices that struts with similar morphology (quadratic structure) but different thickness. In three animals, six coronary arteries were treated with ArterioSorb. At different six animals, six coronary arteries were treated with Absorb. Following three-dimensional(3D) reconstruction of the coronary arteries, Newtonian steady flow simulation was performed and the ESS were estimated. Mixed effects models were used to compare ESS distribution in the two devices. There were 4591 struts in the analyzed 477 cross-sections in Absorb (strut thickness = 157 µm) and 3105 struts in 429 cross-sections in ArterioSorb (strut thickness = 95 µm) for the protrusion analysis. In cross-section level analysis, there was significant difference between the scaffolds in the protrusion distances. The protrusion was higher in Absorb (97% of the strut thickness) than in ArterioSorb (88% of the strut thickness). ESS was significantly higher in ArterioSorb (1.52 ± 0.34 Pa) than in Absorb (0.73 ± 2.19 Pa) (p = 0.001). Low- and very-low ESS data were seen more often in Absorb than in ArterioSorb. ArterioSorb is associated with a more favorable ESS distribution compared to the Absorb. These differences should be attributed to different strut thickness/strut protrusion that has significant effect on shear stress distribution.