Background Flooding has negative impact on agriculture. The plant hormone ethylene is involved in plant growth and stress responses, which are important role in tolerance and adaptation regulatory mechanisms during submergence stress. Ethylene signaling crosstalk with gibberellin signaling enhances tolerance in lowland rice (Flood Resistant 13A) through a quiescence strategy or in deepwater rice through an escape strategy when rice is submerged. Information regarding ethylene-mediated priming in submergence stress tolerance in rice is scant. Here, we used 1-aminocyclopropane-1-carboxylic acid, an ethylene precursor, to evaluate the response in submerged rice seedlings. Results The germination rate and mean germination times of rice seeds was higher in seedlings under submergence only when ethylene signaling was inhibited by supplemented with silver nitrate (AgNO 3 ). Reduced leaf chlorophyll contents and induced senescence-associated genes in rice seedlings under submergence were relieved by pretreatment with an ethylene precursor. The ethylene-mediated priming by pretreatment with an ethylene precursor enhanced the survival rate and hydrogen peroxide (H 2 O 2 ) and superoxide (O 2 − ) anion accumulation and affected antioxidant response in rice seedlings. Conclusions Pretreatment with an ethylene precursor leads to reactive oxygen species generation, which in turn triggered the antioxidant response system, thus improving the tolerance of rice seedlings to complete submergence stress. Thus, H 2 O 2 signaling may contribute to ethylene-mediated priming to submergence stress tolerance in rice seedlings. Electronic supplementary material The online version of this article (10.1186/s12284-019-0284-z) contains supplementary material, which is available to authorized users.