Introduction: Physical fitness is associated with the positive health status of children and is predictive of an adult's health-risk profile. Research suggests that the physical fitness levels of Australian children have rapidly declined in the past two decades. The objective of this study is to provide a rationale and intervention description for an innovative 8-week school-based health-related fitness (HRF) program for primary school students. Methods: The study design will be a group randomised controlled trial with a wait-list control group involving 4 schools in the Hunter Region. At baseline, primary school students, parents and teachers will complete a survey to determine their perceptions of fitness testing and its value in the primary school PDHPE curriculum. Students will also participate in a battery of health-related fitness tests to determine baseline fitness levels. The “Fit 4 Fun” program will be delivered by the classroom teacher during the weekly timetabled PDHPE lesson. “Fit 4 Fun” will be a comprehensive unit of work developed and based on the NSW Board of Studies K-6 Syllabus content and outcomes for stage 3. The unit will promote and involve students participating fitness-based activities at lunch and recess, interactive home and family fitness activities and integration activities with other subjects. On completion of the program and at 6-month follow-up students will complete post-tests to determine changes in HR fitness, activity levels and attitudes to fitness. Students, parents and teachers will also be involved in a process evaluation aimed at examining their perceptions of the value and success of the program.