The literature contains limited evidence on how our brains control eccentric movement. A higher activation is expected in the contralateral motor cortex (M1) but consensus has not yet been reached. Therefore, the present study aimed to compare patterns of M1 activation between eccentric and concentric movements. Nine healthy participants performed in a randomized order three sets of five repetitions of eccentric or concentric movement with the dominant elbow flexors over a range of motion of 60° at two velocities (30°/s and 60°/s). The tests were carried out using a Biodex isokinetic dynamometer with the forearm supported in the horizontal plane. The peak torque values were not significantly different between concentric and eccentric movements (p = 0.42). Hemodynamic responses of the contralateral and ipsilateral M1 were measured with a near-infrared spectroscopy system (Oxymon MkIII, Artinis). A higher contralateral M1 activity was found during eccentric movements (p = 0.04, η² = 0.47) and at the velocity of 30°/s (p = 0.039, η² = 0.48). These preliminary findings indicate a specific control mechanism in the contralateral M1 to produce eccentric muscle actions at the angular velocities investigated, although the role of other brain areas in the motor control network cannot be excluded.