A fundamental approach for resolving motor deficits in patients suffering from various neurological diseases is to improve the impaired cortical function through the modulation of plasticity. In order to advance clinical practice in this regard, it is necessary to better understand the interactions that occur between functional neuromuscular activity and the resulting cortical plasticity. This study tested whether the voluntary contraction of an antagonist muscle modulates the plasticity-like effect of continuous theta burst stimulation (cTBS) recorded from the agonist. The effects of various opposing torques produced by the antagonist were also measured. As a result, the suppressing effect of cTBS was enhanced by mild antagonist contraction, whereas effortful antagonist contraction suspended the plasticity caused by cTBS. In contrast, the antagonist contractions right after cTBS did not significantly influence the effect of cTBS. The results indicate that the antagonist activity alters the effect of cTBS, especially in protocols with synchronous magnetic stimulation and antagonist contraction. Such modulation on cTBS may be through a reciprocal mechanism within the motor cortex, although the spinal regulation of the motoneuronal pool cannot be fully excluded. The present findings are beneficial for elucidating the mechanism of neuromuscular control and for resolving related neurological disorders.