Cortical spreading depolarization (CSD), a slowly propagating wave of transient cellular depolarization, is a reliable cortical response to various brain insults (stroke, trauma, seizures) and underlying mechanism of migraine aura. Little is known about CSD effects on brain network activity. Using undirected (mutual information, MI) and directed (transfer entropy, TE) measures, we studied the dynamics of cross-hemispheric connectivity associated with the development of unilateral CSD in freely behaving rats and the involvement of inhibitory transmission in mechanisms of the coupling changes. We show that the development of CSD in the cortex of one hemisphere is followed by the transient loss of undirected functional connectivity (MI) between ipsilateral and contralateral cortical regions. The post-CSD functional disconnection of the hemispheres was accompanied by an increase in driving force from an unaffected contralateral cortex to an affected one (TE). Mild cortical disinhibition produced by pretreatment with an inhibitory receptor blocking agent (penthylenetetrazole) did not affect CSD but attenuated (MI) or eliminated (TE) the CSD-induced connectivity changes. The effects of CSD on functional connectivity in awake rodents were similar at the individual and group levels, suggesting that the described connectivity response may be a promising network biomarker of CSD occurrence in patients. Author Summary Cortical spreading depolarization (CSD), a wave of transient cellular depolarization, is a universal brain response to acute insults and an underlying mechanism of migraine aura. Here, we studied the effects of a single unilateral CSD induced in awake animals on cross-hemispheric functional connectivity. CSD was followed by a reversible loss of undirected functional connectivity between the affected and unaffected cortices. The post-CSD disconnection was accompanied by an increased driving force from the unaffected cortex to the affected one. The CSD-induced changes in undirected and directed connectivity were attenuated or abolished by a pharmacological blockade of intracortical inhibition. Thus, transient unilateral disfunction rapidly activates network mechanisms of inhibitory restraint from the intact to the dysfunctional hemisphere, indicating a remarkable functional flexibility of awake brain networks.