The novel features characters in their teens dealing with the awkward years between childhood and adulthood. While their situation is far more dire and dangerous than the average teenager's, many of their struggles mirror the everyday struggles that teens face everywhere. The Maze itself can be seen as a metaphor for the confusion young adults face as they begin to navigate their own lives and the real worlds. The Maze has no solution and no seeming way out until Thomas shows the Gladers a different way of looking at the Maze. The way out is one they may have all suspected for quite some time. The Griever Hole is the most frightening way out. The Gladers are forced to face their own doubts and fears to move past it, just as teenagers have to get past their own fears to achieve real growth.
The novel also thematically deals with the issue of authority and how to overcome it one must frequently create their own order and authority. Well-meaning adults use authority to control their children and keep them safe. It is only when that child is able to maintain control and discipline in their own lives that they can throw off the shackles of an outside authority. In this manner, Thomas also struggles with his own issues with becoming an authority figure. The responsibility on him frightens him but he rises to accept it.
Romantic feelings are also a common trope in coming of age stories. Thomas begins to develop romantic feelings for Teresa, though he is unsure of how to handle these feelings. He and Teresa come to be seen as a couple, and Thomas starts to see Chuck as a younger brother. This family structure demonstrates growth on Thomas's part as well. He goes from wanting to escape the Glade and its inhabitants to becoming a surrogate father figure.