Purpose: To evaluate the aqueous humor pharmacokinetics of a preservative-free 0.005% latanoprost unit-dose eye drop (test drug) compared with that of a benzalkonium chloride (BAK)-preserved 0.005% latanoprost branded product (control drug) following topical application to rabbits. Methods: A total of 120 healthy New Zealand albino rabbits were administrated test eye drops (T group) or control eye drops (C group) for a comparative pharmacokinetics study. The aqueous humor was collected at 0.5, 1, 1.5, 2, 3, 4, 6, 8, 12, and 24 h after a single dose or multiple doses. Ultraperformance liquid chromatography-tandem quadrupole mass spectrometry was employed to detect latanoprost free acid (LTA, the active metabolite of latanoprost) in the aqueous humor. Results: For the single-dose study, there was no significant difference (t-test, P > 0.05) in the peak concentration (Cmax) of LTA in aqueous humor between the T group (69.0 ± 23.4 ng/mL) and C group (73.8 ± 28.7 ng/mL). The area under the curve values over 12 h (AUC0-12h) of LTA for the 2 groups were 254.4 (ng/mL) × h and 219.5 (ng/mL) × h, respectively. For the multidose study, there was also no significant difference (t-test, P > 0.05) in the Cmax of LTA in the aqueous humor between the T group (86.8 ± 21.2 ng/mL) and C group (70.5 ± 25.9 ng/mL). The AUC0-12h values of LTA for the 2 groups were 274.5 (ng/mL) × h and 256.3 (ng/mL) × h, respectively. Conclusions: The preservative-free 0.005% latanoprost unit-dose eye drops demonstrated similar pharmacokinetic properties to the BAK-preserved branded product following topical application to rabbits.