Waterlogging is a major abiotic stress affecting crop production worldwide. Wheat is vulnerable to waterlogging, especially during its reproductive stage. Stress priming has been proven to enhance plant tolerance to stress recurring at later growth stages. In this study, two wheat varieties, Yangmai 20 (YM20) and Jimai 22 (JM22), were primed with 2-d waterlogging at four-leaf stage to determine its effect on the tolerance to waterlogging stress at the heading stage. It showed that priming significantly elevated the activities of antioxidant and fermentation enzymes, as well as soluble sugar content, while decreasing soluble protein content in seedlings. Inducible aerenchyma formation was observed in YM20, but not in JM22, as a result of priming. Four genes associated with aerenchyma formation, XET (xyloglucan endotransglycosylase), CEL (endoglucanase), RBOH2 (respiratory burst oxidase homolog 2), and ARF1 (auxin-responsive factor 1), were upregulated in response to priming. Plants of both varieties, primed at the four-leaf stage, exhibited enhanced tolerance to waterlogging at the heading stage, as evidenced by a less decrease in leaf chlorophyll content, grains per spike, thousand-grain weight, and grain weight per spike in comparison with the control, with YM20 showing a more pronounced effect compared to JM22. However, under non-waterlogged conditions at the heading stage, priming induced a slight reduction in grains per spike and grain weight. These findings provide novel insights into the role of stress priming in alleviating the damage caused by waterlogging.