- Thomas (Named after Thomas Edison): The main protagonist of the series. A teenage boy who is a Runner in the Glade. He discovered he had a part in helping WICKED and building the Maze when he was stung by a Griever. He has the ability to speak telepathically with Aris and Teresa. The tattoo on the back of his neck given to him by WICKED researchers says, "To be killed by Group B". Thomas struggles with many conflicts throughout the book, such as becoming the real leader, being betrayed by Teresa, and most importantly, surviving the Scorch. This causes him to become confused and hurt.
- Teresa Agnes (Named after Mother Teresa): Cares for Thomas, as she was his close friend before the trials. She can speak telepathically with Thomas and Aris. She spends much of the novel with Group B, of which she becomes the leader. She gets under the control of WICKED at times and even kisses Thomas, which makes it difficult for Thomas to trust her. She was to be known as "The Betrayer".
- Newt (Named after Isaac Newton): A boy with long, blonde hair, a slight limp, a muscular build, and a strange accent (which is presumed to be British). Newt is a kind and level-headed character, who takes care of the other surviving gladers. Newt is especially close with Thomas, but is also friends with Minho, Frypan, and the rest of the boys in their group. The tattoo on the back of his neck designates him as "The Glue" because he holds them all together.
- Minho: A teenage boy who was the Keeper of the Runners in the Glade. He is aggressive, stubborn, and sassy, which gets him in trouble frequently. He is friends with Newt, Thomas, and all the other Gladers. The tattoo on the back on his neck shows WICKED intended for him to be "The Leader".
- Frypan: A boy who escaped the maze. He was the Glade's cook and is always careful with food. He is described as dark skinned and hairy with a beard though he is still a teenager.
- Aris Jones: Another boy who was involved with WICKED before the Maze. His role in his group was similar to that of Teresa's. He can speak telepathically with Thomas and Teresa and his best friend, Rachel, who was killed when Group B escaped their Maze. The tattoo on his neck designates him as "The Partner".
- Jorge: A man who presents himself as the leader of the Cranks. He appears to be dangerous and psychotic, yet also humorous. He is a father-figure towards Brenda. He helps the Gladers to get past the Scorch and expects a cure for himself and Brenda.
- Brenda: A very handsy girl from Canada, who claimed to be turning into a Crank. Both Jorge and Brenda help lead the Gladers through the Scorch. Brenda leads Thomas after they become separated from the rest of the group. Brenda has a crush on Thomas and flirts with him consistently. However their relationship is soured after drugs cause her to act on her feelings and him to insult her.
- Rat Man: The first WICKED researcher to identify himself to the Gladers. He informs them that they are infected with the Flare and how to get its cure. In The Death Cure, Rat Man is identified as Assistant Director Janson.
- Ava Paige: The chancellor of WICKED who is responsible for arranging for teenagers to be sent to the Maze for study into research for a cure for the Flare.
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