A plant factory forms a closed ecosystem unaffected by external weather and can control environmental variables (temperature, relative humidity, light, etc.). Currently, plant factories equipped with artificial lighting are in the limelight as a means of sustainable agricultural development. However, the efficient irrigation method for seedling production needs to be improved in a closed-type cultivation system. A study was conducted to reveal the appropriate irrigation regime through a comparison of the growth of the seedlings and the water use efficiency when scions and rootstocks of tomato and hot pepper are cultivated in the plant factory with artificial lighting. Water treatment was set to 100% of the moisture content level of the plug tray's weight when each tray's topsoil was sufficiently wet, and irrigation was performed when the water content level reached 80%, 70%, 60%, and 50%. The dry matter production of tomato scions was the highest in the 70% treatment, and rootstocks were the highest in the 50% treatment. However, the water use efficiency of tomato scions and rootstocks was the highest in the 70% and 50% treatments, respectively. The dry matter production of hot pepper scions was the highest in the 50% and 70% treatments, and hot pepper rootstocks were the highest in the 80% treatment. The water use efficiency of hot pepper scions and