Crop yields have been affected by many different biotic and abiotic factors. Generally, plants experience more than one stress during their life cycle, and plants can tolerate multiple stresses and develop cross-tolerance. The expected rise in atmospheric CO2 concentration ([CO2]) can contribute to cross-tolerance. Priming is a strategy to increase yield or to maintain yield under stress conditions. Thus, our objective was to evaluate if priming the rice plants with water deficit during the vegetative stage can induce tolerance to heat stress at anthesis and to evaluate the contribution of e[CO2]. The experiment was arranged in a completely randomized design in a factorial arrangement. Factor A consisted of the following treatments: water deficit at four-leaf stage (no-stress, and drought stress), heat at anthesis (normal temperature, high temperature), and priming with water deficit at four-leaf stage and heat stress at anthesis; and Factor B was two [CO2] treatments: a[CO2] = 400 ± 40 μmol mol-1 and e[CO2] = 700 ± 40 μmol mol-1. We assessed the effect of the treatments on plant growth, yield, biochemical, and transcriptome alterations. Although e[CO2] affected rice growth parameters, it did not affect the priming effect. Primed plants showed an increase in yield and number of panicles per plant. Primed plants showed upregulation of OsHSP16.9A, OsHSP70.1, and OsHSP70.6. These results showed induced cross-tolerance. Water deficit at the rice vegetative stage reduces the effect of heat stress at the reproductive stage. Water deficit at the vegetative stage can be used, after further testing in field conditions, to reduce the effect of heat stress during flowering in rice.