ABSTRACT Purpose To investigate the clinical features of endogenous Klebsiella pneumoniae endophthalmitis (EKPE) and the molecular characteristics of pathogenic K. pneumoniae. Methods A retrospective study was conducted between January 2014 and January 2021. Clinical data were extracted. K. pneumoniae isolates cultured from EKPE patients’ specimens were characterized by antimicrobial susceptibility testing, multilocus sequence typing, capsular serotyping, and virulence gene profiles. Virulence phenotypes were confirmed by mouse lethality assay. Results Thirty-nine patients (47 eyes) were diagnosed with EKPE. Administration of systemic antibiotics and eye treatment within 24 hours of ocular symptom onset was statistically associated with better visual outcomes (p = .007). Sixteen K. pneumoniae isolates were collected, three of which were carbapenem-resistant and avirulent. Only salmochelin encoding gene was harbored by all isolates. Conclusions Systemic and eye treatment administered within 24 hours from the onset improves visual prognosis. Besides hypervirulent strains, avirulent carbapenem-resistant K. pneumoniae can cause EKPE.