Novel clade 2.3.2.1e A(H5N1) virus was detected in cerebrospinal fluid but not in respiratory, rectal-swab and blood samples of an eight-year-old boy presenting with meningoencephalitis without respiratory symptoms. Cerebrospinal fluid A(H5N1)-hemagglutinin-specific antibody levels were higher than that of sera. Clinicians should be aware of emerging clade 2.3.2.1e A(H5N1) associated meningoencephalitis.