Zebrafish was firstly applied to an experimental model for scuticociliatosis caused by Philasterides dicentrarchi, a facultative parasitic ciliate in cultured marine fish. The susceptibility of zebrafish to infection of P. dicentrarchi was assessed by intraperitoneal injection of the ciliates, which produced typical symptoms of scuticociliatosis and significant mortality. The potential use of zebrafish as a model to evaluate the vaccine efficacy against scuticociliatosis was analyzed by immunization of zebrafish with the ciliates lysate. Furthermore, the effect of different adjuvants, such as Quillaja saponin (QS), Montanide, and Freund’s incomplete adjuvant (FIA) on the protective efficacy of the vaccine was investigated. Groups of zebrafish injected with QS or Montanide alone showed higher survival of fish against challenge test compared to control fish. The results suggest that adjuvant-mediated enhancement of innate immune responses play important roles in protection of fish against scuticociliatosis. The considerably high survival in the fish immunized with the antigen alone indicates that the ciliate lysate itself is highly immunogenic to zebrafish, which can elicit protective immune responses. The protective potential of the antigen, ciliate lysate, was enforced through combined administration with adjuvants including QS, Montinide and FIA. No or low mortalities in the groups of fish immunized with the antigen plus adjuvants suggests that the adaptive immune responses of zebrafish might be accelerated by the adjuvants or the protective potential of the antigen and adjuvants might synergistically interact. In spite of several shortcomings such as difficulties in sampling of serum and leucocytes enough to routine immunological analyses, zebrafsih might be the most convenient experimental animal for scuticociliatosis.