The purpose of this study was to report a case of bilateral sequential stromal microsporidiosis that was managed with medical treatment. A 12-year-old male presented with a 2-week history of redness, pain, and dense anterior stromal corneal infiltrate. He was successfully managed with 0.02% topical chlorhexidine gluconate two hourly and topical fluconazole 0.3% six times a day and later, 0.5% loteprednol etabonate was given for a total of 12 weeks. There was complete resolution of the infection with corneal nebular scarring with no episodes of recurrence at 6 months of follow-up. The final best corrected visual acuity was 20/30. The diagnosis of microsporidia can be challenging, and repeated corneal scraping should be attempted in cases with a high index of suspicion. Medical therapy can prove successful in selected cases where early detection of causative organism is done.