Energy literacy is indispensable for a sustainable society, which is fostered and improved by formal and informal energy education. To achieve the goal of energy education, which develops a well-informed public with positive attitudes toward energy conservation and the ability to make appropriate decisions regarding future energy choices, we must understand the status of students' energy literacy and its conceptual structure. By employing and modifying the energy literacy framework and instrument developed by DeWaters & Powers (2013), energy literacy and its structural model for students in Japan were investigated through a survey for 1316 lower secondary students (ages 13-15) in 2014. It was found that female students and students who have family discussions about energy-related issues scored higher than their counterparts. Students in Fukushima scored lower than those in Tokyo and Kyoto/Nagasaki. The energy literacy structure model was described by six predictors by structure equation modeling, where energy-saving behavior was predicted by both the awareness of consequences and the ascription of responsibility. Both the awareness of consequences and the ascription of responsibility were predicted by basic energy knowledge through the cognition of environmental issues. The prediction of energy-saving behavior by the awareness of consequences indicates the role of bonding between the relevant knowledge on energy and the environmental issues and energy-saving behavior. A moderation analysis found that (1) the effect of the cognition of environmental issues on responsibility depends on gender, and the magnitude of its effect did not necessarily depend on the amount of knowledge; (2) the indirect effect of responsibility toward energy-related issues on energy-saving behavior through energy-use conscious behavior seems to decrease with grade progression; and (3) the indirect effect of the awareness of consequences on energy-saving behavior through energy-use conscious behavior depends on the region.