Endophthalmitis, an intraocular infection, may lead to irreversible loss of vision. Antimicrobial chemotherapy is prescribed prior to ocular surgical procedures to avoid endophthalmitis. Fluoroquinolones are the most commonly prescribed and used antibiotics during such procedures. However, the selection of a single entity and proper regimen is not specified in medical guidelines. The objective of this study is to develop a rapid and selective simultaneous high-performance liquid chromatography-tandem mass spectroscopic method to explore the bioavailability of 4 fluoroquinolones, including 0.5% moxifloxacin hydrochloride, 0.3% gatifloxacin, 0.3% ciprofloxacin hydrochloride, and 0.3% ofloxacin, in human aqueous humor after antibiotic topical administration using gemifloxacin as Internal Standard according to the European Medicines Agency (EMA) and US Food and Drug Administration (FDA) guidelines. The newly validated method was capable of accurately and precisely quantifying each antibiotic at the lowest reported lower limit of quantification of 10 ng/mL and operating on a very low pipetting volume of 15 μL, indicating a reliable quantitation of all analytes simultaneously using a very small quantity of aqueous humor with total chromatographic run time of 2.5 min. Sixty-seven patients were divided into 4 groups for each antibiotic. Before the cataract surgery, each group received 4 drops of one of the antibiotics over 1 h, separated by 15 min time interval. After 15–20 min from the last drop, approximately 50–100 μL of aqueous humor was collected during surgery for analysis. The average concentrations of moxifloxacin, gatifloxacin, ofloxacin and ciprofloxacin in aqueous humor samples were 891.8, 271.7, 191.4 and 69.5 ng/mL, respectively. Only moxifloxacin average concentration was higher than the minimum inhibitory concentration for the common endophthalmitis pathogens.