Circular RNAs (circRNAs) constitute a distinctive subclass of RNAs characterized by their covalently closed loop structure, playing regulatory roles in fundamental cellular processes. Due to their increased stability and ubiquitous expression in major tissues and organs, circular RNAs have been widely studied as potential molecular targets in various diseases, including in Parkinson’s Disease (PD) and other neurodegenerative diseases. However, a comprehensive understanding of the precise involvement of circRNAs in the progression of PD has been lacking. In this study, we have utilized large-scale, longitudinal, and deep RNA-seq data from two independent cohorts, namely the Parkinson’s Progression Marker Initiative (PPMI) and the Parkinson’s Disease Biomarker Program (PDBP), to characterize circRNA expression in patients of early PD stage. We identified 12 circRNAs that were found differentially expressed in PD patients over time. Additionally, we were able to map a competing endogenous RNA (ceRNA) network with potential downstream miRNA-mRNA targets and, with the help of co-expression analysis, to identify genes associated with PD progression. Our findings provide compelling evidence for a dysregulated circRNA interactome as an indicator of disease progression. Changes in the expression of some of this interactome’s key molecules, including circRNAs, miRNAs, and gene targets, are significantly associated with PD hallmarks, pathways, and/or changes in UPDRS III scores in PD patients.