The objective of this study was to determine the efficacy and safety of topical tacrolimus compounded in the Pharmacy Service for the treatment of subepithelial corneal infiltrates (SEIs) secondary to adenoviral keratoconjunctivitis. This retrospective study included patients who had been dispensed topical tacrolimus for the treatment of SEIs during the previous year. Patients were treated with tacrolimus 0.03% eye drops twice daily or tacrolimus 0.02% ointment once daily. The following data were recorded: length of treatment, visual acuity before and after treatment, intraocular pressure before, during, and at the end of treatment, previous treatments, and the presence of SEIs after treatment. The subjective symptoms of the patients were also assessed. Fifty-five patients (85 eyes) were included, 54.5% with bilateral involvement. A total of 31 (36.5%) eyes were treated with tacrolimus ointment and 54 eyes (63.5%) with tacrolimus eye drops. The median length of treatment was 185 days (p25-75: 93.5-426), and the mean follow-up duration was 363 days (p25-75: 148-540). In 62.35% of the eyes, the SEIs were reduced in number and size, and in 31.76%, they were eliminated. The patients had better visual acuity after treatment with highly statistically significant differences. Tolerance was good overall, being better in the eye drops group. Topical tacrolimus, compounded in the pharmacy, seems to be an effective and safe alternative for the treatment of SEIs secondary to adenovirus keratoconjunctivitis.