Background <p>Bacterial endogenous endophthalmitis (BEE) represents a rare but severe ophthalmological emergency which caused by hematogenous spread of bacterial infection. As its characteristics of insidious onset and rapid progression, BEE may lead to vision loss or even enucleation without immediate treatments. In recent years, with increasing numbers of immunosuppression and prevalence of resistant strains, incidence of BEE has risen, and its diagnosis and treatment face new challenges.</p> Case presentation <p>A 15-year-old female patient was admitted to department of ophthalmology due to blurred vision and photophobia and lacrimation in the left eye for two days, and was first diagnosed as endophthalmitis and secondary glaucoma. During the diagnosis and treatment process, after smear culture of left chamber and vitreous aspirates, as well as the metagenomic next-generation sequencing (mNGS), final diagnosis of infectious endophthalmitis secondary to <i>Neisseria meningitidis</i> (<i>N. meningitidis</i>) was decided and a targeted treatment plan was developed. After intraocular injection and systemic antibiotic therapy, the patients was discharged after full control of the infection and improved endophthalmitis. Combined with literature review, this study discussed the application value of mNGS in diagnosing endogenous endophthalmitis.</p> Conclusion <p>mNGS shows significant value in the diagnosis of endogenous endophthalmitis in terms of improving positive rate of pathogen detection in intraocular fluid of infectious endophthalmitis and providing strong support for clinical treatments. The successful treatment of this case further confirms the promise of mNGS in ophthalmic infectious diseases. With the continuous progress of technology, mNGS is expected to be popularized and applied in more medical institutions to benefit more patients.</p>