Changes in muscle activation and performance were studied in healthy men in response to 5 weeks of resistance training with or without "eccentric overload". Subjects, assigned to either weight stack (grp WS; n = 8) or iso-inertial "eccentric overload" flywheel (grp FW; n = 9) knee extensor resistance training, completed 12 sessions of four sets of seven concentric-eccentric actions. Pre- and post-measurements comprised maximal voluntary contraction (MVC), rate of force development (RFD) and training mode-specific force. Root mean square electromyographic (EMG(RMS)) activity of mm. vastus lateralis and medialis was assessed during MVC and used to normalize EMG(RMS) for training mode-specific concentric (EMG(CON)) and eccentric (EMG(ECC)) actions at 90°, 120° and 150° knee joint angles. Grp FW showed greater (p < 0.05) overall normalized angle-specific EMG(ECC) of vastii muscles compared with grp WS. Grp FW showed near maximal normalized EMG(CON) both pre- and post-training. EMG(CON) for Grp WS was near maximal only post-training. While RFD was unchanged following training (p > 0.05), MVC and training-specific strength increased (p < 0.05) in both groups. We believe the higher EMG(ECC) activity noted with FW exercise compared to standard weight lifting could be attributed to its unique iso-inertial loading features. Hence, the resulting greater mechanical stress may explain the robust muscle hypertrophy reported earlier in response to flywheel resistance training.