Chorioamnionitis is caused by intrauterine infection with microorganisms including Candida albicans (C. albicans). Chorioamnionitis is associated with postnatal intestinal pathologies including necrotizing enterocolitis. The underlying mechanisms by which intra-amniotic C. albicans infection adversely affects the fetal gut remain unknown. Therefore, we assessed whether intra-amniotic C. albicans infection would cause intestinal inflammation and mucosal injury in an ovine model. Additionally, we tested whether treatment with the fungistatic fluconazole ameliorated the adverse intestinal outcome of intra-amniotic C. albicans infection. Pregnant sheep received intra-amniotic injections with 107 colony-forming units C. albicans or saline at 3 or 5 days before preterm delivery at 122 days of gestation. Fetuses were given intra-amniotic and intra-peritoneal fluconazole treatments 2 days after intra-amniotic administration of C. albicans. Intra-amniotic C. albicans caused intestinal colonization and invasive growth within the fetal gut with mucosal injury and intestinal inflammation, characterized by increased CD3(+) lymphocytes, MPO+ cells and elevated TNF-alpha and IL-17 mRNA levels. Fluconazole treatment in utero decreased intestinal C. albicans colonization, mucosal injury but failed to attenuate intestinal inflammation. Intra-amniotic C. albicans caused intestinal infection, injury and inflammation. Fluconazole treatment decreased mucosal injury but failed to ameliorate C. albicans-mediated mucosal inflammation emphasizing the need to optimize the applied antifungal therapeutic strategy.