To evaluate the alterations in brain dynamics in patients suffering from brainstem or cerebellar infarctions and their potential associations with cognitive function. In this study, 37 patients were recruited who had acute cerebellar infarction (CI), 32 patients who had acute brainstem infarction (BsI), and 40 healthy controls (HC). Every participant had their resting-state electroencephalogram (EEG) data captured, and the EEG microstates were analyzed. The cognitive function was measured by the Neuropsychological Cognitive Scale including the Mini-Mental State Examination (MMSE), the Montreal Cognitive Assessment (MoCA), the Boston Naming Test (BNT), the Digit Span Test (Digitspan), and the Symbol Digit Modalities Test (SDMT). Compared with the HC group, the transition probabilities from Microstate A(MsA) and MsD to MsC significantly decreased while the transition probabilities from MsA to MsD and from MsD to MsB significantly increased in the BsI group. By contrast, the CI group showed a significant increase in transition probabilities from MsA and MsD to MsC, whereas the transitions from MsD to MsB significantly decreased. Subgroup analysis within the CI group demonstrated that the CI patients with dizziness showed increased coverage and duration in MsB but decreased MsD occurrence than those of CI patients with vertigo. In addition, the BsI patients with pons infarction performed a decreased transition probability between MsA and MsD than those of BsI patients with medulla oblongata infarctions. Moreover, the changes in Microstate (Ms) were significantly correlated with cognitive scales in patients with CI or BsI. Altered brain dynamics in patients with CI or BsI suggested that disturbances in resting brain networks might play a functional role in the cognitive impairment of the CI or BsI patients. Through the use of microstate analysis, the dizziness or vertigo following CI could be differentiated. These findings may serve as a powerful tool in our future clinical practices.