Low energy availability (LEA) has been associated with several physiological consequences, but its impact on sleep has not been sufficiently investigated, especially in the context of young athletes. This study examined the potential association between energy availability (EA) status and objective sleep quality in 42 male rugby players (mean age: 16.2 ± 0.8 years) during a 7-day follow-up with fixed sleep schedules in the midst of an intensive training phase. Participants’ energy intake was weighed and recorded. Exercise expenditure was estimated using accelerometry. Portable polysomnography devices captured sleep on the last night of the follow-up. Mean EA was 29.3 ± 9.14 kcal·kg FFM−1·day−1, with 47.6% of athletes presenting LEA, 35.7% Reduced Energy Availability (REA), and 16.7% Optimal Energy Availability (OEA). Lower sleep efficiency (SE) and N3 stage proportion, along with higher wake after sleep onset (WASO), were found in participants with LEA compared to those with OEA (p = 0.04, p = 0.03 and p = 0.005, respectively, with large effect sizes). Segmented regression models of the EA-sleep outcomes (SE, sleep onset latency [SOL]), WASO and N3) relationships displayed two separate linear regions and produced a best fit with a breakpoint between 21–33 kcal·kg FFM−1·day−1. Below these thresholds, sleep quality declines considerably. It is imperative for athletic administrators, nutritionists, and coaches to conscientiously consider the potential impact of LEA on young athletes’ sleep, especially during periods of heavy training.