Chlorogenic acid (CGA), one of the most common phenolic acids, is found in many food and traditional Chinese herbs. Various bioactivities of CGA are studied. However, little is known about these properties of Flos Lonicerae extracts and the difference in the effect between Flos Lonicerae extracts and CGA has not been reported. CGA was identified in Flos Lonicerae extracts by HPLC and determined qualitatively by Quadrupole Ion Trap Mass Spectrometry. In this study, we evaluated the effect of Flos Lonicerae extracts and CGA on inflammatory-related gene expression, adhesion molecule expression and reactive oxygen species (ROS) production in perfluorooctane sulphonate (PFOS)-treated human umbilical vein endothelial cells (HUVECs). The suppression of transcription of IL-1β, IL-6, COX-2 and P-Selectin genes with Flos Lonicerae extracts was greater than that of CGA in PFOS-treated HUVECs, while the degree of suppression on PFOS-induced expression of NOS3 and ICAM-1 was greater for CGA. Furthermore, the suppressive effect of Flos Lonicerae extracts on adhesion of monocytes onto PFOS-induced HUVECs was greater than that of CGA. In addition, Flos Lonicerae extracts and CGA were highly effective in reducing ROS although their effects were almost comparable. So, Flos Lonicerae extracts exhibited antioxidant activity and CGA was a major contributor to this activity. These results suggest that Flos Lonicerae extracts could be useful to prevent PFOS-mediated inflammatory diseases.