Background Conventional corticosteroid therapy after laser epithelial keratomileusis (LASEK) is topical application of 0.1% fluorometholone eye drops for 4 months, but this therapy increases the ocular hypertension risk and leads to poor compliance in patients. It is necessary to explore a safe and effective brachytherapeutic drug. Objective This study was to compare the clinical outcomes between the brachytherapy of 0.5% loteprednol etabonate eye drops and the long-term therapy of 0.1% fluorometholone eye drops after LASEK. Methods Clinical data were retrospectively analyzed from 208 right eyes in 208 mild and moderate myopia patients who received LASEK at Peking University Third Hospital from 2009 to 2013. The eye drops of 0.5% loteprednol etabonate was used 6 times daily since operation day until postoperative day 5, and 4 times daily for a week, and then tapered for three consecutive weeks in 104 eyes of the loteprednol group after LASEK, and 0.1% fluorometholone eye drops was applied topically 4 times daily for initial one month and then tapered for three consecutive months in another 104 eyes in the fluorometholone group after LASEK. Corneal epithelial healing time was compared between the two groups by recording the wearing duration of corneal contact lens. Noncontact intraocular pressure (IOP) was detected and corrected 5 days, 2 weeks, 1 month and 3, 6 months after LASEK. Haze was scored based on the criteria of Cheng under the slit lamp microscope and apparently optometry was performed 1 month and 3, 6 months after LASEK. Results The number of eyes removed corneal contact lens in 5, 6 and 7 days after LASEK was not significantly different between the loteprednol group and the fluorometholone group (χ2=1.180, P=0.554). No considerable differences were seen in the eye numbers with the equivalent spherical lens (absolute value) ≤0.5 D in 1 month, 3 months and 6 months after LASEK (Z=-1.028, P=0.304; Z=-0.398, P=0.691; Z=-0.445, P=0.656). In the fifth days after surgery, the median corrected IOP was 13.52 mmHg and 13.12 mmHg in the loteprednol group and the fluorometholone group, respectively, showing a significant difference between them (Z=-1.985, P=0.047), but no significant differences were found in IOP in 2 weeks, 1 month and 3 months, 6 months after surgery between the two groups (all at P>0.05). IOP elevated (postoperative IOP-preoperative IOP≥5 mmHg) after LASEK in 5 eyes in the loteprednol group and 4 eyes in the fluorometholone group (χ2=0.116, P=0.733). In 1 month after surgery, the number of eyes in different grades of haze was significantly decreased in the loteprednol group compared with the fluorometholone group (χ2=13.506, P=0.009), however, there was no significant differences in haze grading in postoperative 3 months and 6 months between the two groups (χ2=2.199, P=0.699; χ2=1.154, P=0.562). Conclusions Brachytherapy of 0.5% loteprednol etabonate eye drops appears to have a similar effect in anti-inflammation and inhibition of haze to the long-term therapy of 0.1% fluorometholone eye drops after LASEK. Furthermore, topical application of 0.5% loteprednol etabonate eye drops dose not increase the risk of ocular hypertension. Key words: Adrenal cortex hormones/therapeutic use; Anti-inflammatory agents/therapeutic use; Keratomileusis, laser epithelial; Myopia/surgery; Postoperative complications/drug therapy; Loteprednol etabonate; Fluorometholone; Eye drops; Comparative study