Here, we report a rare case of recurrent fungal keratitis (FK) post-amniotic membrane transplantation (AMT) for corneal perforation. A 75-year-old female who had undergone systemic 15 mg prednisolone administration for interstitial pneumonia developed FK in her left eye following treatment for herpetic epithelial keratitis at another clinic. The FK was effectively cured via an oral and local antifungal treatment. However, 1 year later, FK recurred in her left eye, and she was subsequently referred to our hospital since fungal infection had penetrated deep into the cornea. Upon examination, her best-corrected visual acuity was 20/20 OD and hand motion OS. Slit-lamp examination revealed infiltration of corneal ulcers and posterior corneal deposits in her left eye, so she was treated with 0.1% miconazole eye drops in addition to oral miconazole and 1% pimaricin ointment. However, corneal perforation occurred 1 week later, so debridement and AMT were performed, which resulted in a successful outcome. At the 4-month postoperative period, the antifungal eye-drop treatment was discontinued due to no clinical signs of infection with scar formation. However, at the 6-month postoperative period, increased white deposits and the emergence of keratic precipitates were observed around the AMT graft. Recurrent FK was suspected, and anterior-chamber irrigation was performed. Immunostaining revealed a yeast-type fungus, and a cultivation test revealed Candida sp. Thus, penetrating keratoplasty was performed, and there has been no recurrence of FK for 1.5 years. In FK cases, AMT should be carefully considered for surgical indications, with strict follow-up in order to detect any possibility of FK recurrence.