Purpose. To compare the consecutive therapeutic effects of 0.05% emulsion and nanoemulsion cyclosporine (CsA) in dry eye patients after short-term treatment with unpreserved 0.1% fluorometholone (FML). Methods. A prospective, randomized, and double-blinded study of dry eye patients was conducted in a single center. Patients were assigned to the nanoemulsion CsA (group 1) and emulsion CsA (group 2) groups. To relieve discomfort, unpreserved 0.1% FML was used in both groups for 4 weeks and then changed to 0.05% CsA for the next 8 weeks. Symptom assessment in dry eye (SANDE) score, tear secretion, tear film breakup time (TBUT), corneal staining score (CSS), meibomian gland dysfunction (MGD) grade, and meibomian gland (MG) expression were evaluated at baseline and at 4 and 12 weeks after treatment. Results. Twenty-four patients completed the treatment (9 and 15 patients in groups 1 and 2); in both the groups, SANDE score, TBUT, MGD grade, and MG expression were significantly improved after treatment with unpreserved 0.1% FML (each p < 0.005 ), and the therapeutic effects were enhanced with changes in nanoemulsion or emulsion CsA compared with baseline (each p < 0.001 ). TBUT and CSS after treatment in group 1 were significantly improved compared to those in group 2 ( p = 0.003 and 0.020, respectively). Conclusion. Consecutive therapeutic effects of nanoemulsion or emulsion CsA after short-term treatment with unpreserved FML were excellent in patients with dry eyes. Topical nanoemulsion CsA showed better improvement in TBUT and OSS than CsA. This trial is registered with KCT0006070.