Millets are rich sources of nutrients that exhibit excellent functional and health benefits. This study aimed to investigate the engineering and physical properties of kodo and little millet kernels, as well as the physicochemical, nutritional, functional, rheological, and thermal properties of their flours, with refined wheat flour used as a control. The physicochemical and functional properties of Kodo and Little millet flours were systematically investigated using standard protocols, including rheological assessment of pasting behavior and color determination via a Chroma meter. According to our results, kodo millet kernel exhibited significantly (p < 0.05) higher geometric mean diameter, thousand kernel weight, and sphericity, whereas little millet kernel showed higher length, porosity, and angle of repose. Refined wheat flour had significantly higher protein content, whereas kodo millet flour had higher fiber and carbohydrate contents. Kodo flour also exhibited higher swelling and solubility indices, while little millet showed superior water absorption, oil absorption, bulk density, and foaming capacity. Little millet had higher protein, fat, and mineral contents, whereas kodo millet exhibited higher fiber and carbohydrate contents. Furthermore, kodo millet flour had higher peak, trough, breakdown, setback, and final viscosities, as well as higher pasting temperature and peak time compared to little millet. The rheological properties such as peak torque, water absorption, stability, softening, and mixing tolerance index were determined to be higher in kodo millet flour as compared to little millet flour. All the millets under study exhibited high nutritional and functional attributes. The underutilized minor millets could be considered for development of functional food for a sustainable approach with maintained human health and minimizing nutritional security. Moreover, the underutilized millet and their nutritional bioavailability and accessibility should be further investigated in future.