Female distance runners are at a high risk for chronic energy deficiency (ED). ED during predominantly high-volume and/or high-intensity training phases may compromise performance. The relationship between pre-season energy status and running performance in female runners across a season is unclear. To test if energy status as defined by resting metabolic rate ratio (RMR) is associated with running performance, female collegiate distance runners (18-25 yr; n = 38) were assessed across 10-12 wks. Energy status, body composition, and 5 km time trial (measure of performance) were assessed pre- and post-competitive season. Runners were categorized at baseline based on pre-season measured-to-Cunningham-predicted RMR: metabolically suppressed (SUP: RMR < 0.92, n = 12) and energy replete (NSUP: RMR ≥ 0.92, n = 26). Repeated measures ANOVA tested effects of pre-season RMR groups, time, and grouptime on performance. Linear regression analysis tested whether factors (body composition or total triiodothyronine, TT) predicted performance across the season. Twenty-one runners (19.6 ± 0.2 yr, 20.2 ± 0.4 kg/m) completed pre- and post-season performance runs. Groups had similar body mass, body mass index, percent body fat, and lean body mass. ANOVA revealed a significant group effect of RMR on running performance, but no effect of time or grouptime. SUP had slower 5 km time trial performance compared to NSUP (22.4 vs. 20.4 min, p = 0.04). Controlling for post-season VOmax, pre-season TT predicted post-season 5 km times (R = 0.614, p = 0.001). Pre-season energy deficient female runners exhibited poorer running performance during a collegiate competitive season compared to pre-season energy replete runners. Early detection of metabolic compensation in runners may be necessary for optimal performance across a competitive season.