Background: It has been noticed that Female Athlete Triad (Fat) and Relative Energy Deficiency (Red-S) in Sport are characterized by the symptoms of impaired endocrine-metabolic function and bone health in female athletes. In addition, it may be evaluated with a qualitative tool, such as Low Energy Availability in Females questionnaire (LEAF-Q) and quantitative measurements: bone mineral density (BMD), resting energy expenditure (REE), body composition, 24-hour dietary recall. Methods: The aim of this study was to assess the prevalence of Triad and Red-S using the LEAF-Q in youth female football players. Additionally, the difference in the BMD, body composition, REE and energy intake (EI) were assessed between the Triad/Red-S risk and not at-risk groups. Results: Almost two thirds (64.7%) of participants are classified as being at-risk for the triad according to their LEAF-Q scores. There were no statistically significant differences (p > 0.05) between most of the values among children from the analyzed groups. There was a statistically significant difference (p < 0.001) between the EI values among girls from the two analyzed groups: at-risk (1,773.18 kcal ± 232.57) and not at-risk (2,054.00 kcal ± 191.39). Girls who did not meet the energy intake recommendations were 10.00 as likely to be in the Triad/Red-S risk group. Conclusion: Early identification of Fat/Red-S symptoms by screening tools such as the LEAF questionnaire is important in protecting young athletes from long-term damage due to the progression of the risk factors associated with the Fat/Red-S.