Background and Objectives: A sustained mismatch between energy intake (EI) and exercise energy expenditure (EEE) can lead to Low Energy Availability (LEA), as well as health and performance impairments characteristic of Relative Energy Deficiency in Sport (RED-S). Research in females has identified specific LEA cut-points for the risks of developing physiological and performance disturbances. Cut-points in males have yet to be evaluated; therefore, this study examined the prevalence of LEA in highly trained male cross-country skiers. The key purpose of this research was to analyze EI, resting energy expenditure (REE), EEE, and energy availability (EA) in highly trained cross-country skiers during the preparation and competition periods. The secondary objective of our study was to evaluate the relative contribution of fats and carbohydrates to EI, REE, and EEE. Materials and Methods: EI was determined by an estimated 24 h diet recall method, REE was assessed by indirect calorimetry, and EEE was estimated from heart rate in 27 cross-country skiers. Results: EI amounted to 4050 ± 797 kcal/day on a typical training day (TD) and 5986 ± 924 kcal/day (p < 0.001) on a typical competition day (CD). REE on TDs (2111 ± 294 kcal/day or 30 ± 6 kcal/day/kg) was higher (p < 0.05) than on CDs (1891 ± 504 kcal/day or 27 ± 7 kcal/day/kg). The EA in the athletes was <15 kcal∙kg FFM^–1·d^–1 on TDs and <65 kcal∙kg FFM^–1·d^–1 on CDs. EI was not optimal, as indicated by low EA throughout TDs (June). This could be associated with insufficient EI along with a high amount of EEE (3690.7 ± 485.2 kcal/day). During the transition from TD to CD, an increase in the contribution of fats to EI and EEE was observed in cross-country skiers. Conclusion: The conception of LEA and REDs and their potential implication for performance is underestimated among coaches and athletes. The importance of appropriate dietary strategies is essential to ensure that enough calories are consumed to support efficient training.