Low energy availability (LEA) is prevalent in active individuals and negatively impacts bone turnover in young females. High‐impact exercise can promote bone health in an energy efficient manner and may benefit bone during periods of LEA. Nineteen regularly menstruating females (aged 18–31 years) participated in two three‐day conditions providing 15 (LEA) and 45 kcals kg fat‐free mass−1 day−1 (BAL) of energy availability, each beginning 3 ± 1 days following the self‐reported onset of menses. Participants either did (LEA+J, n = 10) or did not (LEA, n = 9) perform 20 high‐impact jumps twice per day during LEA, with P1NP, β‐CTx (circulating biomarkers of bone formation and resorption, respectively) and other markers of LEA measured pre and post in a resting and fasted state. Data are presented as estimated marginal mean ± 95% CI. P1NP was significantly reduced in LEA (71.8 ± 6.1–60.4 ± 6.2 ng mL−1, p < 0.001, d = 2.36) and LEA+J (93.9 ± 13.4–85.2 ± 12.3 ng mL−1, p < 0.001, d = 1.66), and these effects were not significantly different (time by condition interaction: p = 0.269). β‐CTx was significantly increased in LEA (0.39 ± 0.09–0.46 ± 0.10 ng mL−1, p = 0.002, d = 1.11) but not in LEA+J (0.65 ± 0.08–0.65 ± 0.08 ng mL−1, p > 0.999, d = 0.19), and these effects were significantly different (time by condition interaction: p = 0.007). Morning basal bone formation rate is reduced following 3 days LEA, induced via dietary restriction, with or without high‐impact jumping in regularly menstruating young females. However, high‐impact jumping can prevent an increase in morning basal bone resorption rate and may benefit long‐term bone health in individuals repeatedly exposed to such bouts.