Asymmetric dopamine loss is commonly found in early Parkinson's disease (PD), but its effects on functional networks have been difficult to delineate in PD patients because of variations in age, disease duration and therapy. Here we used unilateral 6-hydroxydopamine-lesioned (6-OHDA) rats and controls and treated them with a single intraperitoneal injection of levodopa (L-DOPA) before performing diffusion weighted MRI and resting state functional MRI (rs-fMRI). In accordance with a neurodegeneration of the nigrostriatal dopaminergic pathway, diffusion tensor imaging showed increased radial diffusivity and decreased fractional anisotropy in the lesioned substantia nigra. Likewise a deterministic connectometry approach showed increase of isotropic diffusion values in the medial forebrain bundle. rs-fMRI showed reduced interhemispheric functional connectivity (FC) between the intact and the 6-OHDA lesioned caudate-putamen. Unexpectedly, there was an increased FC between the 6-OHDA lesioned caudate-putamen and sensorimotor cortices of both hemispheres. L-DOPA reversed the FC changes between the dopamine denervated caudate-putamen and the sensorimotor cortices, but not the reduced interhemispheric FC between caudate-putamina. Similarly, L-DOPA induced c-fos expression in both sensorimotor cortices, but only in the dopamine-depleted caudate-putamen. Taken together, these data suggest that asymmetric degeneration of the nigrostriatal dopamine pathway results in functional asynchrony between the intact and 6-OHDA-lesioned caudate-putamen and increased interhemispheric synchrony between sensorimotor cortices. The results also indicate that the initial effect of L-DOPA is to restore functional corticostriatal connectivity rather than synchronize caudate-putamina.