This study investigated sex differences in, and the effect of protein supplementation on, whole-body protein turnover during a military field exercise. Forty-four British Army trainees (14 women) completed a 36-h field exercise. Participants consumed their habitual diet (n = 14 women [Women], protein intake 1.7 g·kg-1·d-1; n = 15 men [Men Controls], protein intake 1.6 g·kg-1·d-1) or the habitual diet and an additional 46.6 g·d-1 protein (n = 15 men [Men Protein], protein intake 2.1 g·kg-1·d-1). Total 24 h whole-body protein turnover was measured using the [15N]-glycine end-product method and muscle protein breakdown was estimated from urinary 3MH:creatinine 24 h before, during, and 96 h after field exercise. Women and Men Protein were compared with Men Controls to examine the effect of sex and protein supplementation. Whole-body protein turnover, synthesis, breakdown, and balance, and 3MH:creatinine did not differ between time-points (p ≥ 0.056). Whole-body protein balance was higher and 3MH:creatinine was lower in Women than Men Controls (all time-points, p ≤ 0.032) with no difference between sexes for other measures of protein turnover (p ≥ 0.072). Men Protein and Men Controls were not different for any outcome (p ≥ 0.060) but adjusted mean differences [95% confidence intervals] showed protein balance was 1.12 [0.28, 1.97] g·kg-1·d-1 higher in Men Protein than Men Controls during the field exercise. Women have higher whole-body protein balance than men in arduous training, likely due to higher energy balance. Protein supplementation may be effective for protecting whole-body protein balance in men.