Extrachromosomal circular DNAs (eccDNAs) have been implicated in the pathogenesis of various diseases, particularly in cancer, where they contribute to gene amplification and oncogene expression. However, the regulatory mechanisms of eccDNAs in type 2 diabetes mellitus (T2DM) during both the early and late stages remain unknown. Here, we employed circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) to identify and analyze eccDNAs in pancreatic islets of T2DM mice at 8- and 24-week time points. As a result, the differentially expressed eccDNAs were 76 and 5422 in the 8- and 24-week groups, respectively. KEGG analysis showed that the glucagon signaling pathway was significantly enriched in the 8-week group. However, in the 24-week group, the pathways were primarily enriched in the phosphatidylinositol signaling system, the Wnt signaling pathway, pathways related to cancer, and the Rap1 signaling pathway. In particular, Wnt7acircle and Brafcircle were significantly up-regulated, potentially contributing to cell proliferation and tumor development. The results of this study indicated that a substantial quantity of eccDNAs was generated during both stages and regulated various biological processes, suggesting that eccDNA accumulation may correlate with the elevated risk of cancer and the emergence of multiple complications in the later stages of T2DM.