Background: Microbial keratitis in children can cause visual loss and amblyopia. In this study, epidemiological features of microbial keratitis in children was examined at a tertiary care center in Iran. Methods: Sixty-three cases of microbial keratitis under the age of 15 admitted at Khalili hospital, Shiraz, Iran, during five years, were reviewed. Patients' age, gender, residential area, ulcer size, causative organism, surgical, and medical treatment were investigated. Results: Mean age of patients was 5.2 ± 4.8 years and 68.2% were under five years old. The prevalence of microbial keratitis was significantly higher in males than females (P = 0.003), especially in children coming from rural areas. Ulcers larger than 5 mm were observed more than smaller ones (P ≤ 0.0001) in hospitalized children. Ocular trauma was the most common risk factor (present in 56.9%), while in 22.4%, no risk factor was detected. The most causative microbial agent was Staphylococcus (42.8%). Fungus was detected in two cases and herpes simplex was suspected in eight cases. In 54% recovery was observed with medical therapy; mainly by combination of cefazolin-gentamicin and ceftazidime-vancomycin drops. Penetrating keratoplasty was needed in 16.9% and conjunctival flap in 14.7% of recalcitrant cases. Overall recovery from microbial keratitis was observed in 72% of cases, who showed complete healing of ulcer or significant decrease in size at the time of discharge from the hospital. Conclusions: Pediatric microbial keratitis was more common under the age of five years old and trauma was the main predisposing factor. Staphylococcus was the main causative microorganism and recovery was observed with topical treatment in the majority of cases. Trauma prevention and timely treatment is recommended.