The Chocolate Waris a rather tightly focused novel with a set of themes that are closely related and interwoven. However, we might reduce the themes down to one potent idea - the cost of individualism.
Within this idea there are others which we can point to as significant themes in the novel. Power and peer pressure are related notions which form the counter-point to Jerry's individualism in The Chocolate War.
Archie, Brother Leon and Emile Janza are each characters expressive of the modes of power on display in the school environment. Peer pressure, authority figures, and bulllies are all part of the power structure which Jerry resists and defies.
Jerry struggles to be strong throughout the novel and his strength is always an inner-strength. From the opening pages where Jerry finds a way to keep picking himself up on the football field to the end where he manages to stand up to Emile Janza and the entire school in a very public way, Jerry's character is exploring the nature of non-conformity and the heavy price that individuals can sometimes be made to pay.
One of The Chocolate War's principle themes is the futility of individual protests and resistance in the face of such power structures and, by implication, the importance of collective action.