Large areas of rainfed lowlands of Asia annually experienced flash flooding during the rice-growing season, which is an important abiotic stress that adversely affect grain yield of rice (Oryza sativa L.) crop. Submergence stress is a common environmental challenge for agriculture sustainability in these areas because lack of high-yielding, flood-tolerant cultivars. In this study, IR64-Sub1 and IR64 were compared for their tolerance to submergence at active tillering (AT), panicle initiation (PI) and heading (H) stages with nitrogen and phosphorus application time. We evaluated the role of cultivars, stage of submergence and N and P application on phenology, leaf senescence (LS), photosynthetic (Pn) rate, yield attributes and yield. Under non-submerged conditions, no difference was observed in phenology, Pn rate and yield of both cultivars. Submergence substantially reduced biomass, Pn rate, yields attributes and yield across cultivars with more drastic reduction in IR64. Submergence at H stage proves to be most detrimental. Nitrogen application after desubmergence with basal P improved the Pn rate resulting in significantly higher yield and yield components. Nitrogen application before submergence resulted in increased LS and ethylene accumulation in shoots leading to drastic reduction in growth, Pn rate and yield. Crop establishment and productivity could therefore be enhanced in areas where untimely flooding is anticipated by avoiding N application before submergence and applying N after desubmergence with basal P (phosphorus).