Minority Francophone students in predominantly English-speaking Canadian provinces tend to perform lower on large-scale assessments of achievement than their Anglophone peers and majority Francophone students in Quebec. This study is the first to apply multilevel modeling methods to examine the extent to which school-level factors may be differentially associated with achievement for minority Francophone students compared to majority Francophone students. Forty-four percent of the variance in science achievement among Francophone schools was explained by the model. After taking into consideration gender as well as student- and school-level socioeconomic status, French-language schools in Ontario and New Brunswick had, on average, lower PISA 2006 science achievement scores compared to schools in Quebec. Findings indicate that differences in performance between linguistic minority and majority Francophone students could not be reduced to differences in socioeconomic status or to the school resource factors investigated in this study.