This study investigated the effects of high-intensity interval training (HIIT) vs. work-matched moderate-intensity continuous exercise (MOD) on metabolism and counterregulatory stress hormones. In a randomized and counterbalanced order, 10 well-trained male cyclists and triathletes completed a HIIT session 81.6 ± 3.7% maximum oxygen consumption (V̇o2 max); 72.0 ± 3.2% peak power output; 792 ± 95 kJ and a MOD session (66.7 ± 3.5% V̇o2 max; 48.5 ± 3.1% peak power output; 797 ± 95 kJ). Blood samples were collected before, immediately after, and 1 and 2 h postexercise. Carbohydrate oxidation was higher (P = 0.037; 20%), whereas fat oxidation was lower (P = 0.037; -47%) during HIIT vs. MOD. Immediately after exercise, plasma glucose (P = 0.024; 20%) and lactate (P < 0.01; 5.4×) were higher in HIIT vs. MOD, whereas total serum free fatty acid concentration was not significantly different (P = 0.33). Targeted gas chromatography-mass spectromtery metabolomics analysis identified and quantified 49 metabolites in plasma, among which 11 changed after both HIIT and MOD, 13 changed only after HIIT, and 5 changed only after MOD. Notable changes included substantial increases in tricarboxylic acid intermediates and monounsaturated fatty acids after HIIT and marked decreases in amino acids during recovery from both trials. Plasma adrenocorticotrophic hormone (P = 0.019), cortisol (P < 0.01), and growth hormone (P < 0.01) were all higher immediately after HIIT. Plasma norepinephrine (P = 0.11) and interleukin-6 (P = 0.20) immediately after exercise were not significantly different between trials. Plasma insulin decreased during recovery from both HIIT and MOD (P < 0.01). These data indicate distinct differences in specific metabolites and counterregulatory hormones following HIIT vs. MOD and highlight the value of targeted metabolomic analysis to provide more detailed insights into the metabolic demands of exercise.