Exercise load is a key component in determining end-point adaptations to resistance exercise. Yet, there is no information regarding the use of different inertia (i.e., loads) during isoinertial flywheel resistance exercise, a very popular high-intensity training model. Thus, this study examined power, work, force, and eccentric overload produced during flywheel resistance exercise with different inertial settings in men and women. Twenty-two women (n = 11) and men (n = 11) performed unilateral (in both legs) isolated concentric (CON) and coupled CON and eccentric (ECC) exercise in a flywheel knee extension device employing 6 inertias (0.0125, 0.025, 0.0375, 0.05, 0.075, 0.1 kg·m). Power decreased as higher inertias were used, with men showing greater (p ≤ 0.05) decrements than women (-36 vs. -29% from lowest to highest inertia). In contrast, work increased as higher inertias were employed, independent of sex (p ≤ 0.05; ∼48% from lowest to highest inertia). Women increased CON and ECC mean force (46-55%, respectively) more (p ≤ 0.05) than men (34-50%, respectively) from the lowest to the highest inertia evaluated, although the opposite was found for peak force data (i.e., peak force increased more in men than in women as inertia was increased). Men, but not women, increased ECC overload from inertia 0.0125 to 0.0375 kg·m2. Although estimated stretch-shorting cycle use during flywheel exercise was higher (p ≤ 0.05) in men (6.6%) than women (4.9%), values were greater for both sexes when using low-to-medium inertias. The information gained in this study could help athletes and sport and health professionals to better understand the impact of different inertial settings on skeletal muscle responses to flywheel resistance exercise.