Rice is a primary food for more than three billion people worldwide and cultivated on about 12% of the world’s arable land. However, more than 88% production is observed in Asian countries, including Pakistan. Due to higher population growth and recent climate change scenarios, it is crucial to get timely and accurate rice yield estimates and production forecast of the growing season for governments, planners, and decision makers in formulating policies regarding import/export in the event of shortfall and/or surplus. This study aims to quantify the rice yield at various phenological stages from hyper-temporal satellite-derived-vegetation indices computed from time series Sentinel-II images. Different vegetation indices (viz. NDVI, EVI, SAVI, and REP) were used to predict paddy yield. The predicted yield was validated through RMSE and ME statistical techniques. The integration of PLSR and sequential time-stamped vegetation indices accurately predicted rice yield (i.e., maximum R2 = 0.84 and minimum RMSE = 0.12 ton ha−1 equal to 3% of the mean rice yield). Moreover, our results also established that optimal time spans for predicting rice yield are late vegetative and reproductive (flowering) stages. The output would be useful for the farmer and decision makers in addressing food security.