Nanoliposomes have an organized architecture that provides versatile functions. In this study, liposomes were used as an ocular carrier for nanogold capped with flucytosine antifungal drug. Gold nanoparticles were used as a contrasting agent that provides tracking of the drug to the posterior segment of the eye for treating fungal intraocular endophthalmitis. The nanoliposomes were prepared with varying molar ratios of lecithin, cholesterol, Span 60, a positive charge inducer (stearylamine), and a negative charge inducer (dicetyl phosphate). Formulation F6 (phosphatidylcholine, cholesterol, Span 60, and stearylamine at a molar ratio of 1:1:1:0.15) demonstrated the highest extent of drug released, which reached 7.043 mg/h. It had a zeta potential value of 42.5±2.12 mV and an average particle size approaching 135.1±12.0 nm. The ocular penetration of the selected nanoliposomes was evaluated in vivo using a computed tomography imaging technique. It was found that F6 had both the highest intraocular penetration depth (10.22±0.11 mm) as measured by the computed tomography and the highest antifungal efficacy when evaluated in vivo using 32 infected rabbits’ eyes. The results showed a strong correlation between the average intraocular penetration of the nanoparticles capped with flucytosine and the percentage of the eyes healed. After 4 weeks, all the infected eyes (n=8) were significantly healed ( P<0.01) when treated with liposomal formulation F6. Overall, the nanoliposomes encapsulating flucytosine have been proven efficient in treating the infected rabbits’ eyes, which proves the efficiency of the nanoliposomes in delivering both the drug and the contrasting agent to the posterior segment of the eye.