This paper uses a fully nonparametric framework to assess the efficiency of primary schools using data about schools in 16 European countries participating in PIRLS 2011. This study represents an original enterprise since most of the empirical research in the field is restricted to evaluations at regional or national level and focused on secondary education. For our purpose, we adapt the metafrontier framework to compare and decompose the technical efficiency of primary schools operating in heterogeneous contexts, which in our case is represented by different educational systems or countries. Likewise, we use an extension of the conditional nonparametric robust approach to test the potential influence of a mixed set of environmental school factors and variables representing cultural values of each country. Our results indicate that the intergenerational transmission of non-cognitive skills like responsibility or perseverance are significantly related to school efficiency, whereas most school factors do not seem to have a significant influence on school performance.