Stenotrophomonas maltophilia has been reported in various ocular infections, including keratitis, conjunctivitis, preseptal cellulitis, and endophthalmitis, all of which may lead to vision loss. However, the S. maltophilia strain is resistant to a wide variety of antibiotics, including penicillins, third-generation cephalosporins, aminoglycosides, and imipenem. In this study, we retrospectively reviewed the clinical characteristics, antibiotic susceptibility, antimicrobial minimum inhibitory concentrations (MICs), and visual outcomes for S. maltophilia endophthalmitis. The data of 9 patients with positive S. maltophilia cultures in a tertiary referral center from 2010 to 2019 were reviewed. Cataract surgery (n = 8, 89%) was the most common etiology, followed by intravitreal injection (n = 1, 11%). S. maltophilia’s susceptibility to levofloxacin and moxifloxacin was observed in 6 cases (67%). Seven isolates were resistant to sulfamethoxazole-trimethoprim (78%). The MIC90 for S. maltophilia was 256, 256, 256, 8, 12, 12, 12, and 8 μg/mL for amikacin, cefuroxime, ceftazidime, tigecycline, sulfamethoxazole-trimethoprim, levofloxacin, galtifloxacin, and moxifloxacin, respectively. Final visual acuity was 20/200 or better in 5 patients (56%). Fluoroquinolones and tigecycline exhibited low antibiotic MIC90. Therefore, the results suggest that fluoroquinolones can be used as first-line antibiotics for S. maltophilia endophthalmitis.