Background: Elizabethkingia meningoseptica meningitis is rare and challenging to manage infection. As this infection is always associated with superimposed multidrug-resistant organisms, a combination and prolonged antibiotic treatment are necessary to ensure the complete eradication of infections. Case Description: We report successful antibiotic therapies in a patient with E. meningoseptica bacteremia and meningitis complicated with superimposed extreme-drug-resistant Acinetobacter baumannii infection in a patient post transsphenoidal hypophysectomy complicated with central venous thrombosis. Conclusion: Antibiotic combination therapy with prolonged duration in those with E. meningoseptica with concomitant multi-resistant organisms is needed. Diagnosing associated prothrombotic risk with the infection and prompt treatment would also be essential.