6-hydroxydopamine (6-OHDA) striatal lesion is a well-established rat model of early-stage Parkinson’s disease. The aim of the study was to compare connectivity patterns between 20 6-OHDA lesion rats and 10 sham controls under urethane anesthesia, modelling natural sleep, by using functional magnetic resonance imaging (fMRI). We found that functional connectivity patterns were disturbed in lesion animals. The decrease in functional connectivity, however, occurred only in rapid eye movement (REM)-like state. Furthermore, thalamocortical functional connectivity was correlating with striatal dopamine depletion ratio, making these changes possible early diagnostic markers for Parkinson’s disease.