T cells primarily drive the autoimmune destruction of pancreatic beta cells in Type 1 diabetes (T1D). However, the profound yet uncharacterized diversity of the T cell populations in vivo has hindered obtaining a clear picture of the T cell changes that occur longitudinally during T1D onset. This study aimed to identify T cell clonal expansion and distinct transcriptomic signatures associated with T1D progression in Non-Obese Diabetic (NOD) mice. Here we profiled the transcriptome and T cell receptor (TCR) repertoire of T cells at single-cell resolution from longitudinally collected peripheral blood and pancreatic islets of NOD mice using single-cell RNA sequencing technology. We detected disease dependent development of infiltrating CD8 + T cells with altered cytotoxic and inflammatory effector states. In addition, we discovered a high frequency of transcriptionally distinct double negative (DN) T cells that fluctuate throughout T1D pathogenesis. This study identifies potential disease relevant TCR sequences and potential disease biomarkers that can be further characterized through future research.