The title "Kingdom Days" may refer to a time of innocence, such as a childhood. But the song also includes references to the Bible and the afterlife. The line "There's a kingdom of love down in your heart" suggests that the only hope for salvation lies in the individual.
Ultimately, the song is about the cost of war and the need to find hope and healing. It is a powerful reminder that the innocent are always the most hurt in times of conflict.