This retrospective study was designed to investigate the incidence, clinical characteristics and prognosis of corneal perforation in patients with fungal keratitis. Clinical data of 648 patients who were diagnosed with fungal keratitis in Air Force General Hospital were obtained in this retrospective study. All participants were divided into the corneal perforation (n=156) and non-perforation groups (n=492). The pathogenesis, etiological characteristics, admission date and clinical symptoms were statistically compared between two groups. Clinical prognosis of patients presenting with corneal perforation was retrospectively analysed. The incidence rate of corneal perforation in patients with fungal keratitis was 23.7%. No statistical significance was noted between two groups in terms of history of corneal trauma (r=0.218, P=0.640), contact lens wear (r=0.268, P=0.605) and ocular surface diseases (r=0.353, P=0.553). The proportion of patients who were topically administered with glucocorticoid (χ2=14.251, P<0.01) and complicated with diabetes mellitus (χ2=22.365, P<0.01) considerably differed between two groups. The type of pathogenic fungus and duration of onset before admission significantly differed between two groups (both P<0.05). In addition, the size of corneal lesion, infiltration depth and hypopyon in the corneal perforation groups were statistically different from those in the non-perforation group (all P>0.05). Fungal keratitis patients who were administered with glucocorticoid and complicated with diabetes mellitus had a higher risk of corneal perforation compared with their counterparts. Type of pathogenic fungus, admission date, size and infiltration depth of corneal lesion and hypopyon probably served as the risk factors of the incidence of corneal perforation in patients diagnosed with fungal keratitis.