Objective To investigate the changes of Galectin-9 (Gal-9) in serum and cerebrospinal fluid in children with viral encephalitis (VE) and to epxplore its potential significance in the diagnosis and prognosis of VE. Methods The levels of Gal-9 in serum and cerebrospinal fluid were detected by enzyme-linked immunosorbent assay double-antibody sandwich and compared in 30children with VE in acute and convalescent phases and in 12 children without VE. Results The differences of Gal-9 levels in serum and cerebrospinal fluid were statistically significant between VE acute phase group and VE recovery phase group as well as control group (F = 92.70, 81.95, P < 0.01). The Gal-9 levels in serum and cerebrospinal fluid of the children in VE acute phase and of the children in VE recovery phase were significantly higher compared to those in the control group (P < 0.01). The levels of Gal-9 in serum and cerebrospinal fluid of children in VE convalescent phase are significantly higher than those in acute phase of VE (P < 0.01). There was a positive correlation between levels of Gal9 in cerebrospinal fluid and in serum (r =0.523, P < 0.01). The levels of SP-D correlated negatively with the total CSF leucocytic count in children of VE (rs= -0.469, P < 0.001). Conclusions Gal-9 played an important role in the later stage of viral encephalitis recovery.