The incidence of microbial keratitis after Intacs implantation is extremely low and channel infection has been infrequently reported. We present a 23-year-old woman with keratoconus of both eyes who underwent implantation of two intrastromal corneal ring segments (Intacs, KeraVision, Inc., Fremont, CA, USA) in the right eye. After 2.5 months, the patient presented with decreased vision, inflammation, and stromal infiltration at the lower channel site of Intacs. Culture was positive for Escherichia coli. The patient was treated with removing of lower segment of Intacs, and subconjunctival and topical antibiotics. The keratitis resolved, leaving opacity and thinning and mild neovascularization in the lower channel site. Our case report illustrates the risk of microbial keratitis even months after Intacs implantation. It shows need for long-term postoperative attention by both patient and physician.