Drought is one of the most serious constraints to rice cultivation, even under alternate wetting and drying (AWD), which is a water-saving management practice. In rice, enhanced root development is essential for stable shoot growth, adaptability and productivity under water deficit environments. We identified and characterized outstanding rooting1 (our1) rice mutant using hydroponics. The present study sought to examine morphological root traits of the our1 mutant and the role of the mutation gene in shoot growth and yield under AWD. Thus, we evaluated the growth performance of the our1 rice mutant in pot experiments and under field AWD conditions in Kenya. The experiments were conducted with our1 mutant, its wild type and their progenies under both AWD and continuously waterlogged (CWL) conditions. The our1 mutant possessed a well-developed root system and exhibited particularly enhanced thin root development, which was maintained from the early vegetative stage through the reproductive stage under both pot and field AWD management. This enhanced root development promoted shoot growth through increased water uptake during rewatered conditions between drought periods in AWD. In addition, the our1 mutant showed enhanced shoot growth during the reproductive stage, resulting in the maintenance of yield under AWD fields. Genotypes harbouring our1 mutation gene showed higher yields compared to wild-type genotypes which was attributed to their higher photosynthetic ability as a result of enhanced root activity. These results suggest the important role of a well-developed root system architecture and enhanced root function in stabilizing rice yields under water-limited environments. Our findings indicate that the our1 mutation gene can serve as a novel breeding material to mitigate the impact of transient drought stress on yield under AWD.