Data on the performance fitness of 50,385 Australian students aged between 12 and 15 years were used to determine whether students differed in physical fitness according to school sector (independent vs government vs Catholic). Students were tested between 1995 and 2001 as part of the Australian Sports Commission's Talent Search program. The results of the 20 m shuttle run (20mSRT), vertical jump and 40 m sprint tests were selected as being representative of aerobic, explosive and anaerobic performance. All results were expressed as age- and gender-specific z-scores. MANOVA showed that independent school students outperformed students from the Catholic and government sectors on the selected tests for both boys and girls (p < 0.0001). In the 20mSRT, the difference amounted to 0.28-0.43 SDs. In the sprint and jump tests, independent school students were superior by 0.05-0.17 SDs. A proxy for socio-economic status (SES) explained about 90% of the differences between sectors, with high SES schools consistently outperforming low SES schools. Nonetheless, even when SES was factored in, sectoral differences remained significant. Insofar as fitness is related to school activities, these findings raise equity concerns in Australian school physical education.