This study investigated sex differences in, and the effect of protein supplementation on, bone metabolism during a 36-hour military field exercise. Forty-four British Army Officer cadets (14 women) completed a 36-hour field exercise. Participants consumed their habitual diet (n = 14 women [Women] and n = 15 men [Men Controls]) or the habitual diet and an additional 46.6 g·d-1 protein in men (n = 15 men [Men Protein]). Women and Men Protein were compared with Men Controls to examine the effect of sex and protein supplementation. Circulating markers of bone metabolism were measured before, 24 hours after (post-exercise), and 96 hours after (recovery) the field exercise. βCTX and cortisol were not different between timepoints or Women and Men Controls (p ≥ 0.094). PINP decreased from baseline to post-exercise (p < 0.001) and recovery (p < 0.001) in Women and Men Controls. PTH increased from baseline to post-exercise (p = 0.006) and decreased from post-exercise to recovery (p = 0.047) in Women and Men Controls. Total 25(OH)D increased from baseline to post-exercise (p = 0.038) and recovery (p < 0.001) in Women and Men Controls. Testosterone decreased from baseline to post-exercise (p < 0.001) and recovery (p = 0.007) in Men Controls, but did not change for Women (all p = 1.000). Protein supplementation in men had no effect on any marker. Men and women experience similar changes to bone metabolism-decreased bone formation and increased PTH-following a short field exercise. Protein had no protective effect likely because of the energy deficit.