Twelve phenolic metabolites (nine ternatin anthocyanins and three glycosylated quercetins) were identified from the blue flowers of Clitoria ternatea by high-performance liquid chromatography diode array detection and electrospray ionization/mass spectrometry (HPLC-DAD-ESI/MS(n)). Three anthocyanins not reported in this species before show fragmentation pattern of the ternatin class. Extracts were fractionated in fractions containing flavonols (F3) and ternatin anthocyanins (F4). In general, C. ternatea polyphenols showed anti-inflammatory properties in lipopolysaccharide (LPS)-induced inflammation in RAW 264.7 macrophage cells with distinct molecular targets. Flavonols (F3) showed strong inhibition of COX-2 activity and partial ROS suppression. On the other hand, the ternatin anthocyanins (F4) inhibited nuclear NF-κB translocation, iNOS protein expression, and NO production through a non-ROS suppression mechanism. Accordingly, quercetin glycosides and ternatin anthocyanins from the blue flower petals of C. ternatea may be useful in developing drugs or nutraceuticals for protection against chronic inflammatory diseases by suppressing the excessive production of pro-inflammatory mediators from macrophage cells.