The effect of neck muscle fatigue induced by prolonged isometric contraction of the neck extensor muscles on self-motion perception was studied. The magnitude of self-motion perception was assessed by evaluating the tracking of a remembered earth-fixed visual target during passive symmetric and asymmetric sinusoidal horizontal body rotation. The trunk was rotated on a stationary head for examining the role of neck proprioception and the whole-body for that of the vestibular system. To induce neck extensor muscle fatigue, participants held their head extended against a load for several minutes. Perceptual responses were examined before and during neck muscle fatigue. It was found that the perception of the movement was diminished by neck muscle fatigue as shown by a reduction of the amplitude of the tracking during trunk rotation. This suggests that fatigue affects the motion perception when the neck proprioceptive system was activated by the rotation. This effect has been observed only during slow rotation, while the responses remained unmodified during fast rotation. In contrast, neck muscle fatigue did not affect the tracking when rotation activated only the vestibular system. Furthermore, neck muscle fatigue abolished the effect of tonic head deviation on perceptual responses to whole-body rotation. Therefore, neck muscle fatigue alters the self-motion perception reducing the ability of the proprioceptive system to signal slow trunk rotations and the position of the head relative to the trunk during body movements.