Increasing night temperatures can reduce growth and yield of rice plants, but limited information is available on the comparative effects of high night temperature (HNT) treatment at different growth stages on growth and physiological responses of rice. We conducted a study in controlled-environment chambers to determine the growth and physiological responses and spikelet differentiation of rice cultivars to HNT treatment at different growth stages. Plants were exposed to two temperatures: 30/21 °C (low) and 30/25 °C (high) day/night temperatures. At the end of the vegetative period, plants grown in the low (LNT) and high (HNT) night temperatures were further subdivided and plants were exposed to different temperature treatments in the reproductive growth period. Photosynthesis, night respiration rates, and plant growth parameters were measured at various stages. High night temperature had no significant effects on the growth of rice cultivars during the vegetative phase. Maximum photosynthesis at the vegetative phase was not significantly affected, but plant dark respiration increased (within the 14–20% range). Genotypic variation in dark respiration was observed at later growth stages. Rice plants that received HNT at the early reproductive stage had the lowest number of spikelets per panicle, presenting a 35.9% of degenerated spikelets, significantly higher than those observed in other treatment times. This study shows that the response of rice cultivars to HNT varies with time of treatment and that the occurrence of HNT during the reproductive period provided supportive evidence on how HNT might reduce yield by increasing plant’s dark respiration rate and spikelet degeneration (which consequently reduced sink size), thus, decreasing biomass production.