Resistant starch (RS) and/or protein consumption favorably influence energy metabolism, substrate utilization, and weight management. The current study administered four different versions of a pancake breakfast containing waxy maize or RS with and without whey protein (WP) and measured postprandial thermogenesis (TEM), fuel utilization, and circulating satiation and appetite factors for 180 min in a group of healthy, adult men. On four separate visits to the laboratory, eight participants were administered four different pancake breakfast meal challenges using a single-blind, randomized crossover design: (1) waxy maize starch (WMS) control; (2) WMS and WP (WMS + WP); (3) RS; or (4) RS and WP (RS + WP). TEM (kcals/180 min) was significantly greater (p < 0.05) in RS + WP (45.11; confidence interval (CI), 33.81–56.41) compared to WMS (25.61; CI, 14.31–36.91), RS (29.44; CI, 18.14–40.74), and WMS + WP (24.64; CI, 13.34–35.94), respectively. Fat oxidation was enhanced (p < 0.05) after RS + WP compared to RS at 60 min (+23.10%), WMS at 120 min (+27.49%), and WMS and WMS + WP at 180 min (+35.76%; +17.31%, respectively), and RER was decreased with RS + WP versus the other three meals (mean differences: ≥−0.021). Insulin concentrations were decreased (p < 0.05) following RS + WP compared to WMS, whereas both RS (−46.19%) and RS + WP (−53.05%) insulin area under the curve (AUC) were greatly reduced (p < 0.01) compared to WMS. While limited by sample size, meals containing both RS and WP increased postprandial thermogenesis and fat oxidation, and lowered insulin response compared to isocaloric meals without this combination. Therefore, RS + WP may favorably impact energy metabolism and thus weight control and body composition under chronic feeding conditions.