BACKGROUND The aim of this study was to investigate whether patients with basal ganglia stroke and patients with pontine stroke have different types of functional connectivity (FC) alterations in the early chronic phase. MATERIAL AND METHODS We included 14 patients with pontine stroke, 17 patients with basal ganglia stroke, and 20 well-matched healthy controls (HCs). All of them underwent resting-state functional magnetic resonance imaging (rs-fMRI) scanning. The independent component analysis (ICA) approach was applied to extract information regarding the default-mode network (DMN), including anterior DMN (aDMN) and posterior DMN (pDMN) components and the sensorimotor network (SMN). RESULTS Compared with HCs, patients with basal ganglia stroke exhibited significantly reduced FC in the left precuneus of the pDMN, right supplementary motor area (SMA), and right superior frontal gyrus (SFG) of the SMN. Additionally, FC in the left medial prefrontal gyrus (MFG) of the aDMN, right precuneus and right posterior cingulate cortex (PCC) of the pDMN, and left middle cingulate gyrus (mid-CC) of the SMN decreased in patients with pontine stroke. CONCLUSIONS The different patterns of FC damage in patients with basal ganglia stroke and patients with pontine stroke in the early chronic phase may provide a new method for investigating lesion-induced network plasticity.