Religion and its various forms is an important motif in War Brothers. Every major character is religious in some way. However, different characters have different religious backgrounds, with some embracing the syncretic combination of traditional Ugandan religion with Christianity, and some embracing Catholicism wholesale. Oteka attends a Catholic church, yet also visits with medicine men and believes in the existence of both traditional magic and Christianity, whereas Jacob and Tony are more purely Catholic.

The Lord’s Resistance Army, on the other hand, represents a sort of twisted mockery of those religious feelings. The Lord’s Resistance Army fights for a theocratic and authoritarian version of Christianity, which involves magic, rituals, and ideas from other belief systems. Unlike the religion of the teenagers, this version of religious thought is explicitly shown to form a system of control, used to brainwash and control the actions of the kidnapped children. After their experiences, some of the teenagers become notably less religious, with Hannah deciding against being a nun and Jacob struggling to find any higher meaning in what happened to him as a child soldier. However, Oteka presents an alternative view, reassuring Jacob that they can transcend their experiences by exercising their God-given right to choose a path of humanity and nonviolence.