Stroke is a major leading cause of chronic disability, often affecting patients’ motor and sensory functions. Functional magnetic resonance imaging (fMRI) is the most commonly used method of functional neuroimaging, and it allows for the non-invasive study of brain activity. The time-dependent coactivation of different brain regions at rest is described as resting-state activation. As a non-invasive task-independent functional neuroimaging approach, resting-state fMRI (rs-fMRI) may provide therapeutically useful information on both the focal vascular lesion and the connectivity-based reorganization and subsequent functional recovery in stroke patients. Considering the role of a prompt and accurate prognosis in stroke survivors along with the potential of rs-fMRI in identifying patterns of neuroplasticity in different post-stroke phases, this review provides a comprehensive overview of the latest literature regarding the role of rs-fMRI in stroke prognosis in terms of motor and sensory outcomes. Our comprehensive review suggests that with the advancement of MRI acquisition and data analysis methods, rs-fMRI emerges as a promising tool to study the motor and sensory outcomes in stroke patients and evaluate the effects of different interventions.