Rice is cataloged as one of the most widely cultivated crops globally, providing food for a large proportion of the global population. Integrating Geographic Information Systems (GISs), such as unmanned aerial vehicles (UAVs), into agricultural practices offers numerous benefits. UAVs, equipped with imaging sensors and geolocation technology, enable precise crop monitoring and management, enhancing yield and efficiency. However, Peru lacks sufficient experience with the application of these technologies, making them somewhat unfamiliar in the context of modern agriculture. In this study, we conducted experiments involving four distinct rice varieties (n = 24) at various stages of growth to predict yield using vegetation indices (VIs). A total of nine VIs (NDVI, GNDVI, ReCL, CIgreen, MCARI, SAVI, CVI, LCI, and EVI) were assessed across four dates: 88, 103, 116, and 130 days after sowing (DAS). Pearson correlation analysis, principal component analysis (PCA), and multiple linear regression were used to build prediction models. The results showed a general prediction model (including all the varieties) with the best performance at 130 days after sowing (DAS) using NDVI, EVI, and SAVI, with a coefficient of determination (adjusted-R² = 0.43). The prediction models by variety showed the best performance for Esperanza at 88 DAS (adjusted-R² = 0.94) using EVI as the vegetation index. The other varieties showed their best performance using different indices at different times: Capirona (LCI and CIgreen, 130 DAS, adjusted-R² = 0.62); Conquista Certificada (MCARI, 116 DAS, R² = 0.52); and Conquista Registrada (CVI and LCI, 116 DAS, adjusted-R² = 0.79). These results provide critical information for optimizing rice crop management and support the use of unmanned aerial vehicles (UAVs) to inform timely decision making and mitigate yield losses in Peruvian agriculture.