Abstract This case report aims to document a case of bilateral endotheliitis occurring shortly after riboflavin-assisted cross-linking (CXL) in a young male patient with progressive keratoconus. The objective is to identify potential risk factors, treatment strategies, and outcomes while considering relevant literature on similar cases. A male in his late adolescence with bilateral progressive keratoconus underwent bilateral CXL using riboflavin and ultraviolet A light exposure. Postoperatively, the patient received moxifloxacin drops, prednisolone acetate drops, and artificial tears. Seven days later, the patient presented with decreased vision, photophobia, and corneal findings consistent with endotheliitis. Treatment with prednisolone acetate and moxifloxacin eye drops was initiated. Two months later, visual acuity deteriorated, but anterior slit-lamp findings improved, and the intraocular pressure measurement was high. Prednisolone acetate was tapered, whereas loteprednol etabonate gel, brimonidine eye drops, and cyclosporine eye drops were initiated. After 7 months, visual acuity improved, and endotheliitis resolved, although mild residual central haze persisted. This case highlights the occurrence of acute idiopathic endotheliitis following routine CXL and its successful management. Although limited cases have been reported, a standardized treatment protocol is lacking. In our patient, the utilization of loteprednol etabonate gel, cyclosporine eye drops, brimonidine eye drops, and regular follow-up examinations led to improved clinical findings and visual acuity. Further studies are warranted to establish optimal treatment approaches for similar cases of endotheliitis following CXL.