The aim of this study was to design and formulate a novel low-irritant NSAIDs ophthalmic emulsion of flurbiprofen axetil (FBA), the prodrug of flurbiprofen (FB). FBA ophthalmic emulsion (FBA-EM) was prepared by high-pressure homogenization with caster oil as oil phase and tween 80 as emulsifying agent. Results from the stability evaluation suggested the protect effect of oil droplets on the stability of FBA. Compared with FBA-oil solution, the AUC(0→10h) of FB in aqueous humor administered in FBA-EMs exhibited 6.7-fold (F2), 4.5-fold (F3) and 4.6-fold (F4) increase. With the increment of oil content, the MRT also prolonged, which of FBA-EM F2-F4 were 5.14 ± 2.23, 5.73 ± 3.35 and 8.71 ± 0.94 h, respectively. No significant difference was found between the ocular bioavailability of FBA-EM F2 and 0.03% FB-Na eye drops. Ocular irritation evaluation revealed that FBA-EM F2 had better ocular biocompatibility than 0.03% FB-Na eye drops, even though the FBA concentration was up to 0.1%. Intraocular anti-inflammation effect evaluation showed that FBA-EM F2 had a quite good anti-inflammation effect. In conclusion, FBA-EM F2 with elevated FBA concentration to be 0.1% might represent a promising NSAIDs ophthalmic emulsion with low irritancy and improved anti-inflammation effect.