Traditional eye drops are convenient to use; however, their effectiveness is limited by their poor retention time and bioavailability in the eyes due to ocular barriers. Therefore, strategies to enhance ocular drug delivery are required. Herein, we constructed a mucin-1 aptamer-functionalized liposome and loaded it with cyclosporin A, a common ocular drug in eye drops used to treat dry eye diseases (DED). Drug encapsulation slightly reduced the liposome size without changing the surface potential of liposomes. Approximately 90% of the cholesterol-modified aptamers were inserted to the liposomes. We evaluated the cytotoxicity, anti-inflammatory effects, cell permeability regulation, and retention time of liposomes in human corneal epithelial cells under dry eye conditions. These results suggest that the aptamer-functionalized liposomes are more efficient as nanocarriers than non-functionalized liposomes and drug-free liposomes. They restore inflammation levels by 1-fold and remain in the cells for up to 24 h. An in vivo study was also performed in a rat DED model, which demonstrated the efficacy of aptamer-functionalized liposomes in restoring tear production and corneal integrity. The present study demonstrated the capability of aptamer-functionalized liposomes in the delivery of ocular drugs for the management of ocular diseases.