Rationale: Sepsis with brain abscess induced by Citrobacter freundii in adults has rarely been reported and is extremely pathogenic with a high mortality rate. Early diagnosis of the infection still remains challenging.Patient Concerns: A 27-year-old woman was transferred to our emergency department for fever, status seizure and refractory hypotension. Administration of midazolam, propofol and sodium valproate could not attenuate the seizure except for the addition of vecuronium. The blood white blood cell count was 42.91 (109/L) with 80% neutrophils, and procalcitonin was 22.46ng/mL.Diagnoses: Both deoxyribonucleic acid and ribonucleic acid of C freundii were detected in blood by metagenomic next-generation sequencing of pathogens,the diagnosis of septic shock and brain abscess caused by C freundii was highly suspected.Interventions: On day 1, antibiotics of cefoperazone sodium and sulbactam sodium 6g/day, immunoglobulin, and hydrocortisone were used with suspected septic shock. Continuous renal replacement therapy was used to eliminate excessive lactate, ammonia, myohemoglobin and creatinine. On day 2, a brain computed tomography scan revealed multiple patchy slightly low densities in the brain, antibiotics were adjusted to meropenem intravenously 3g/day.Outcomes: On day 2, a brain computed tomography scan revealed multiple patchy slightly low densities in the brain, she died on day 3.Lessons: Clinicians should consider the possibility of brain abscess when evaluating a patient with new-onset dizziness, fever, seizure, or other neurologic symptoms or signs, especially for patients whose mental status changes. metagenomic next generation sequencing and resistance genes could be considered when cerebrospinal fluid or blood results are negative and clinical manifestations are highly suspected of infection or when the treatment time is limited.