The functional relevance of cortical reorganization post-stroke is still not well understood. In this study, we investigated task-specific modulation of cortical connectivity between neural oscillations in key motor regions during the early phase after stroke. EEG and EMG recordings were examined from 15 patients and 18 controls during a precision grip task using the affected hand. Each patient attended two sessions in the acute and subacute phase (median of 3 and 34 days) post-stroke. Dynamic causal modelling (DCM) for induced responses was used to investigate task-specific modulations of oscillatory couplings in a bilateral network comprising supplementary motor area (SMA), dorsal premotor cortex (PMd) and primary motor cortex (M1). Fourteen models were constructed for each subject, and the input induced by the experimental manipulation (task) was set to inferior parietal lobule (IPL). Bayesian model selection favoured a fully connected model. A reduced coupling from SMA and intact M1 in the γ-band (31–48 Hz) to lesioned M1 in the β-band (15–30 Hz) was observed in patients in the acute phase compared to controls. Behavioural performance improved significantly in the subacute phase, while an increased positive coupling from intact PMd to lesioned M1 and a less negative modulation from lesioned M1 to intact M1 were observed for patients compared to controls both from the γ-band to the β-band. We infer that the observed differences in cross-frequency cortical interactions are important for functional recovery.