Recent studies suggest that CNS phospholipase A2 (PLA2) isoforms play a role in nociception, but until now, direct evidence of increased brain PLA2 activity during allodynia or hyperalgesia is lacking. The present study was carried out, using lipidomics or systems wide analyses of lipids using tandem mass spectrometry, to elucidate possible changes in rat brain lipids after inflammatory pain induced by facial carrageenan injection. The caudal medulla oblongata showed decreases in phospholipids including phosphatidylethanolamine and phosphatidylinositol species, but increases in lysophospholipids, including lysophosphatidylethanolamine, lysophosphatidylinositol and lysophosphatidylserine, indicating increased PLA2 activity and release of arachidonic acid after facial carrageenan injection. These changes likely occur in the spinal trigeminal nucleus which relays nociceptive input from the orofacial region. High levels of sPLA2-III, sPLA2-XIIA, cPLA2 and iPLA2 mRNA expression were detected in the medulla oblongata. Increase in sPLA2-III mRNA expression was found in the caudal medulla of carrageenan-injected rats, although no difference in sPLA2-III protein expression was detected. The changes in lipids as determined by lipidomics were therefore consistent with an increase in PLA2 enzyme activity, but no change in enzyme protein expression. Together, these findings indicate enhanced PLA2 activity in the caudal medulla oblongata after inflammatory orofacial pain.