Locomotor coordination depends on precise and appropriate adjustments of intra- and interlimb muscle activity phasing. Muscle coordination deficits, in the form of inappropriately phased muscle activity patterns, are well recognized in both the paretic and non-paretic limbs of stroke survivors. Our recent work demonstrated that muscle phasing can be systematically influenced by changing the relative angular positions of limbs in both neurologically intact individuals and people post-stroke. However, it is still unknown whether the observed transient changes in adjusted muscle phasing can be adapted following a short-bout of training on the split-crank ergometer. To explore the extent to which the non-paretic and paretic limbs of people with stroke can adapt to new muscle activity phasing changes, we examined the adaptation of muscle phasing following a short-bout of pedaling training at two specific relative spatial angular positions of limbs that had caused the greatest phasing changes in our previous studies. Twelve individuals with post-cerebral stroke and twelve age- and gender-matched control subjects participated in this study. We demonstrated that both intact and cerebrally impaired nervous systems are capable of adapting new muscle phasing patterns and producing aftereffects that persisted for at least 10 min. However, we observed a completely different trend of aftereffects in post-stroke subjects compared with controls. Specifically, in controls, the aftereffects were observed only in the leg that was in the following position during the adaptation training whereas in post-stroke subjects, aftereffects were observed only in the leg that acted as the leading leg during adaptation, regardless of the limb being paretic or non-paretic. These findings suggest that adapting a new muscle activity pattern during a bilateral locomotor task depends mainly on the relative temporal position of contralateral limb.