Female endurance athletes are considered a high-risk group for developing Relative Energy Deficiency in Sport (REDs). Due to the lack of educational and behavioral intervention studies, targeting and evaluating the effects of the practical daily management of REDs, we developed the Food and nUtrition for Endurance athletes—a Learning (FUEL) program, consisting of 16 weekly online lectures and individual athlete-centered nutrition counseling every other week. We recruited female endurance athletes from Norway (n = 60), Sweden (n = 84), Ireland (n = 17), and Germany (n = 47). Fifty athletes with symptoms of REDs and with low risk of eating disorders, with no use of hormonal contraceptives and no chronic diseases, were allocated to either the FUEL intervention (n = 32) (FUEL) or a 16-week control period (n = 18) (CON). All but one completed FUEL, while 15 completed CON. We found strong evidence for improvements in sports nutrition knowledge, assessed via interviews, and moderate to strong evidence in the ratings concerning self-perceived sports nutrition knowledge in FUEL versus CON. Analyses of the seven-day prospective weighed food record and questions related to sports nutrition habits, suggested weak evidence for improvements in FUEL versus CON. The FUEL intervention improved sports nutrition knowledge and suggested weak evidence for improved sports nutrition behavior in female endurance athletes with symptoms of REDs.