Yak-Kong (YK), a small black soybean (Glycine max) in Korea, contained higher concentrations of antioxidants than ordinary black soybean or yellow soybean in our previous study. We prepared the fermented YK extract by using a novel lactic acid bacterium, Pediococcus pentosaceus AOA2017 (AOA2017) isolated from Eleusine coracana, and found that the antioxidant ability was enhanced after fermentation. In order to investigate the cause of the enhanced antioxidant ability in the fermented YK extract, we conducted a phenolic composition analysis. The results show that proanthocyanidin decreased and phenolic acids increased with a statistical significance after fermentation. Among the phenolic acids, p-coumaric acid was newly produced at about 11.7 mg/100 g, which did not exist before the fermentation. Further, the fermented YK extract with increased p-coumaric acid significantly inhibited the lipopolysaccharide-induced THP-1 monocyte–endothelial cell adhesion compared to the unfermented YK extract. The fermented YK extract also suppressed the protein expression levels of vascular cell adhesion molecule (VCAM)-1 in human umbilical vein endothelial cells (HUVECs). Together with the previous studies, our results suggest that the extract of YK fermented by AOA2017 has potential to be a new functional food material with its enhanced bioactive compounds which may help to prevent atherosclerosis caused by oxidative stress.