Purpose: To compare the costs associated with medications and travel of patients with smear-proven bacterial keratitis and fungal keratitis in a tertiary care center in India. Methods: Retrospective analysis of case records of a cohort of patients who presented between April 2017 and March 2018 to a tertiary care center in India, with infectious keratitis who were smear-positive for bacteria or fungi, and whose costs of treatment and travel were supported by a philanthropic program. Results: In total, 672 case records of 177 smear-positive bacterial keratitis (BK) and 495 smear-positive fungal keratitis (FK) were included in the study. Further, 62% of BK and 75% of FK received more than one antimicrobial drug ( P < 0.001). The mean total medication cost (INR) was significantly more in FK (959.1 ± 675.2) compared to BK (674.9 ± 463.7) ( P < 0.0001). The mean medication cost (INR) per visit was also more for FK (201.1 ± 109.4) compared to BK (155.2 ± 84.1) ( P < 0.0001). The mean total medication cost was significantly more for FK for both patients who healed with medical treatment (611.6 ± 395.6 for BK, 801.5 ± 599.9 for FK, P = 0.0005) and for patients who required TPK (953.7 ± 653.1 for BK, 1374.6 ± 701.5 for FK, P = 0.0023) compared to their respective counterparts in BK Conclusion: Patients with fungal keratitis incurred significantly more on medications compared to patients with bacterial keratitis irrespective of whether they had healed with successful medical treatment or required therapeutic keratoplasty. Prolonged duration of treatment and the high costs of antifungal medications account for the significant economic burden of fungal keratitis.