Oxygen depletion due to submergence causes cellular energy starvation and severely restricts the growth of most plant species. To survive hypoxic and anoxic environments under submergence, rice (Oryza sativa L.) possesses various adaptive mechanisms including energy production from seed storage starch via anaerobic respiration and coleoptile elongation during early post-germinative growth. However, further investigation of the submergence tolerance mechanism is important for understanding its effect on plant physiology and agricultural production. Here, we found that pretreatment of rice seeds with organic acids, such as citrate and lactate, improved subsequent seedling growth under submergence. Citrate pretreatment promoted coleoptile elongation under submergence. Moreover, the expression of genes related to anaerobic respiration and phenylpropanoid biosynthesis was activated in the embryo of citrate treated seeds during submergence while the expression of genes encoding starch degradation enzymes and signaling factors was not significantly influenced. Accordingly, starch and soluble sugar amounts in the endosperm were not altered by citrate pretreatment. These results suggest that citrate pretreatment promotes coleoptile elongation in rice seeds under submergence via the transcriptional regulation of genes related to anaerobic energy production, possibly through an unknown mechanism related to phenylpropanoid metabolism.