Background <p>Microsporidial keratoconjunctivitis is a rare but serious ocular infection that can occur in contact lens wearers, particularly in individuals exposed to certain environmental or behavioral risk factors. Early and accurate diagnosis is crucial to ensure effective treatment and prevent long-term complications. This report presents a case of bilateral microsporidial keratoconjunctivitis in a pediatric patient who wore orthokeratology lenses, accompanied by a review of relevant literature.</p> Case presentation <p>A 9-year-old female presented with bilateral eye redness and a persistent foreign body sensation lasting for 3 weeks. The patient had recently started raising a pet parrot at home. Upon examination, conjunctival congestion was observed, along with papillary and follicular hypertrophy and diffuse punctate staining of the corneal epithelium. Corneal scraping and gene sequencing confirmed the diagnosis of <i>Encephalitozoon</i> hellem infection.</p> Conclusion <p>This case underscores the rare occurrence of bilateral microsporidial keratoconjunctivitis in an immunocompetent child wearing orthokeratology lenses. Environmental exposure and lens wear may have contributed to infection. Clinicians should consider microsporidiosis in the differential diagnosis of persistent keratoconjunctivitis that does not respond to conventional therapies.</p>