We have compared functional MRI signals in primary sensorimotor cortex (SM1) during a paced motor task of each hand before and after unimanual (right hand) fatiguing exercise. Our aims were to determine whether the degree of activation is different when a motor task is performed after a fatiguing exercise, and whether there are any differences in activation between movement of the fatigued and non-fatigued hands. There was a significant reduction in the number of voxels activated in SM1 in the hemisphere contralateral to movement of both the fatigued hand (38 +/- 5 pre-exercise versus 21 +/- 3 post-exercise; P < 0.05) and the non-fatigued hand (32 +/- 4 pre-exercise vs 18 +/- 4 post-exercise; P < 0.05). There was no significant difference in the magnitude of the functional magnetic resonance imaging signal before or after exercise, however, the variance increased significantly after exercise (6.0 +/- 0.5 pre-exercise vs 7.3 +/- 0.6 post-exercise; P < 0.01). Reduced functional activation in SM1 may reflect increased variability in the activation rather than a reduction in activation of cortical motor networks after fatigue.