This paper reports a death due to septic shock caused by Shewanella algae bloodstream infection and Epstein-Barr virus (EBV) co-infection in an elderly male patient who had no history of seawater exposure. Shewanella algae was identified in blood culture. Antimicrobial susceptibility testing showed that the strain was susceptible to meropenem while resistance to ceftriaxone. EBV sequence was detected by metagenomic next-generation sequencing (mNGS) of blood specimen. Despite meropenem combined with antiviral and anti-shock treatment, the patient still rapidly progressed to multiple organ failure and died. This case suggests that Shewanella algae infection relevant to freshwater environment exposure should be alerted, co-infection with EBV can exacerbate the severity of sepsis, and potential risk of treatment failure should be paid attention in clinical practice despite carbapenems susceptibility confirmed by testing.