In order to search for new effective Schistosoma japonicum vaccine candidate genes and study its immune protection against challenge infection in mice, S. japonicum adult worm cDNA library was screened with sera from rabbits immunized with S. japonicum female worm antigen. The novel gene (designated Sj-F1, GenBank accession number are AY261995) was cloned into the prokaryotic expression vector pTWIN1 and the eukaryotic expression vector pcDNA3 respectively. The positive recombinants were identified by PCR and restriction enzyme digestion. The plasmid pTWIN1/Sj-F1 was transformed into E.coli ER2566. The soluble recombinant fusion protein (rSj-F1/intein2) was expressed in E. coli under low IPTG concentration and low temperature, then analyzed by SDS-PAGE and Western blot. The plasmid pcDNA3/Sj-F1 was transformed into E.coli ER2502 for preparing DNA vaccine. Mice were immunized with rSj-F1 protein or/and pcDNA3/Sj-F1 DNA vaccine. Two weeks after the third vaccination, a challenge infection was carried out with S. japonicum cercariae. Worms and eggs collected from the livers of mice were counted 42 days after challenge infection. Levels of specific antibody were detected by ELISA before infection. Immunization experiment showed the recombinant Sj-F1 protein with FCA adjuvant or with chitosan adjuvant provided 28.07%, 24.69% worm reduction rates and 48.30%, 46.38% egg reduction rates in mice respectively. The naked pcDNA/Sj-F1 provided 18.47% worm reduction rate and 35.06% egg reduction rate. The worm and egg reduction rates were increased to 40.42%, 42.38% and 56.17%, 62.87% respectively when mice were immunized with the pcDNA/Sj-F1 at priming and with rSj-F1 by subcutaneously or intranasally at booster. The results suggest that both recombinant Sj-F1 protein and naked DNA can induced partial protection immunity against S. japonicum infection and the protection can be enhanced via DNA priming and rSj-F1 boosting.