After spinal cord injury (SCI), reorganization processes and changes in brain connectivity occur. Besides the sensorimotor cortex, the subcortical areas are strongly involved in motion and executive control. This exploratory study focusses on the cerebellum and vermis. Resting-state functional magnetic resonance imaging (fMRI) was performed. Between-group differences were computed using analysis of covariance and post-hoc tests for the seed-based connectivity measure with vermis and cerebellum as regions of interest. Twenty participants with complete SCI (five subacute SCI, 15 with chronic SCI) and 14 healthy controls (HC) were included. Functional connectivity (FC) was lower in all subjects with SCI compared with HC in vermis IX, right superior frontal gyrus (pFDR = 0.008) and right lateral occipital cortex (pFDR = 0.036). In addition, functional connectivity was lower in participants with chronic SCI compared with subacute SCI in bilateral cerebellar crus I, left precentral- and middle frontal gyrus (pFDR = 0.001). Furthermore, higher amplitude of low-frequency fluctuations (ALFF) was found in the left thalamus in individuals with subacute SCI (pFDR = 0.002). Reduced FC in SCI indicates adaptation with associated deficit in sensory and motor function. The increased ALFF in subacute SCI might reflect reorganization processes in the subacute phase.