Omeprazole is the first of a class of medications that inhibit gastric secretion by changing the activity of H+ / K+ -ATPase in the gastric parietal cells, which is the final stage in acid secretion. It is currently commercially available in an oral dosage form. It has a low bioavailability of 30-40% and short half-life. In this study, non-ionic microemulsions containing omeprazole were produced and characterized for transdermal and intranasal application. The droplet size, rheological characteristics, poly disparity index, flow through skin, and in vivo bioavailability of the microemulsions were all measured. Except for one of the created microemulsions, all formulations demonstrated Newtonian viscosity and had droplet size smaller than 200 nm, the skin permeation of microemulsions containing omeprazole through excised rat epidermis showed flux ranging between 9.945 and 0.86 µg.cm-2h-1. The in vivo study showed that the intranasal and transdermal percentage relative bioavailability in comparison to an oral solution were 329% and 103 %, respectively. The produced formulations were stable microemulsions that could serve as good carriers and promising formulations for omeprazole delivery via transdermal and intranasal routes.