Introduction Reducing fat mass (FM) while retaining fat free mass (FFM) is a common goal of athletes. Evidence suggests that some - but not all - forms of intermittent energy restriction (IER) may be superior to the conventional method of continuous energy restriction (CER) for people with excess body fat that are sedentary, by reducing some of the adaptive responses to ER. However, it is yet to be established whether this dietary approach is effective for athletes. Methods and analysis A single-blind, parallel group, randomised controlled trial with a 1:1 allocation ratio is proposed. Sixty healthy athletes aged ≥18 years will be recruited from local sporting facilities and randomised to an intervention of either moderate CER (mCER) or moderate IER (mIER). Both interventions will consist of 12 weeks of moderate ER, plus 3 weeks in energy balance (EB). The mCER intervention will entail 12 weeks of continuous moderate ER, followed by 3 weeks in EB. The mIER intervention will entail 12 weeks of moderate ER, administered as 4×3 week blocks of moderate ER, interspersed with 3×1 week blocks of EB. The co-primary outcomes are changes in FM and FFM after 12 weeks of moderate ER. Secondary outcomes will be changes in FM and FFM at 15 weeks after intervention commencement, as well as muscle performance, physical activity, sleep quality, changes in resting energy expenditure, subjective drive to eat, circulating concentrations of appetite-regulating hormones, mood states and diet acceptability. Trial registration ACTRN12618000638235p.