The annual National Assessment Program—Literacy and Numeracy (NAPLAN) measures the literacy and numeracy skills of primary and secondary students in Australia. Under the three Smarter Schools National Partnership, additional funding is provided to the independent schools with the expectation of improving student performance. Using multilevel modelling to account for within-school variables and demographics, we analyse NAPLAN data from the 2008–2011 tests for a sample of independent schools to estimate the effect of the National Partnerships on student performance. The results indicated that on average male students performed higher in the numeracy test but scored lower in each of the literacy tests. Aboriginal and Torres Strait Islander students scored lower in numeracy, reading, writing, and grammar and punctuation. Students from low socioeconomic status schools performed lower in writing.