Neospora caninum is an obligate intracellular protozoan parasite responsible for heavy economic losses in dairy and beef cattle farms worldwide. Although vaccination is widely regarded as the preferable strategy to prevent neosporosis no commercial vaccine is currently available. We have previously shown that intranasal immunization with an N. caninum antigen extract enriched in hydrophobic proteins plus CpG adjuvant protected mice against intragastrically established neosporosis. Nevertheless, the antigen specificity as well as the long-term protective effect of this immunization strategy were not determined. Here, we show that the protective effect of this intranasal immunization procedure lasted for at least 20weeks. Protection was accompanied by long-lasting elevated levels of parasite-specific serum IgG and intestinal IgA. Moreover, spleen and mesenteric lymph node cells obtained from non-infected long-term immunized mice responded by producing interferon-γ following in vitro parasite-antigen recall. Analysis of serum IgG and intestinal IgA antibody reactivity in immunized mice identified dense granule antigen 7 (NcGRA7) and microneme associated protein 1 (NcMIC1) as immunodominant antigens respectively recognized by those antibody fractions. In summary, this work shows that a previously reported mucosal immunization strategy against N. caninum infection established through the gastrointestinal tract is effective in the long term.