In recent years, food irradiation using gamma-rays is one of the most valuable practices for insect disinfestation in rice grains for extended shelf life. In this study, flours from four pigmented rice cultivars were exposed to gamma-irradiation using Co-60 at different doses (0, 5, 10, and 15 kGy). The impact of gamma-irradiation on the physico-chemical, functional, and morphological characteristics of pigmented rice flours were analyzed. Results revealed that reduction in amylose content, pH, bulk density, tapped density, and syneresis, while solubility, water absorption capacity, and swelling power values increased significantly (p < 0.05). Pasting characteristics of pigmented rice flours also reduced after exposure to gamma-irradiation. Morphological features of pigmented rice flour granules revealed no evidence of physical destruction after irradiation except for black kavuni flour. The structural analysis by FTIR confirms no effect of gamma-irradiation on pigmented rice flours. Overall, the study revealed that irradiated pigmented rice flours with enhanced functional properties of less than 10 kGy can be effectively used in the development of value-added rice-based food products considering all the beneficial and safety aspects.