A Separate Peace contains a variety of themes including:

• The search for identity: Both Finny and Gene seem to be exploring what it means to be developing into a man during a war-time era. One pursues sport whereas the other prefers academics. As they each make effort to cross into the others area of expertise, conflicts arise. (i.e. Finny tries to train Gene for the Olympics that aren't going to happen, but Gene lets him try anyway.)
• Alienation: Leper purposefully leaves the school to hide from the duty to go to war. To then admit to Gene why he left is difficult. Gene struggles with the knowledge that he hurt his friend and he wonders how many of the others know for sure what he did.
• Quest for purpose: Finny struggles to know what to do with himself since he cannot participate in the war, something very physical. He spent his childhood preparing his body, and now that body is broken.
• Friendship: Gene and Finny struggle with truth and acceptance, tolerance and happy mediums. Even in the closest of relationships, people manipulate each other. Forgiveness is hard to come by.
• Jealousy: Finny is jealous of Gene's health. Gene is jealous of Finny's incredibly contagious character. Gene is likely concerned that he may have acted on his jealousy.

In addition, Enotes has prepared the attached link about other themes in this book.