Sixty-seven patients with first acute ischemic stroke onset between 3 to 7 days and 25 age- and sex- matched controls were analyzed for the performance of a resting-state functional MRI to investigate whether the functional connectivity (FC) of the motor network in acute ischemic stroke is independently associated with functional outcomes. The FC of cortical motor network and default mode network was analyzed. The FC was compared between controls, patients with favorable outcomes (modified Rankin Scale, mRS ≤1), and patients with unfavorable outcomes (mRS ≥2) at 3 months. Of the 67 patients, 23 (34%) exhibited unfavorable outcomes. In multivariate analysis, the FC between ipsilesional primary motor cortex (M1) and contralesional dorsal premotor area (PMd) ≤0.63, were independently associated with unfavorable outcomes (odds ratio = 6.32, P = 0.032), whereas the FC of default mode network was not different between groups. The interhemispheric FC of the motor network is an independent predictor of functional outcomes in patients with acute ischemic stroke.