20th Century Fox confirmed their faith in The Maze Runner as a franchise and acquired the rights to the second book, The Scorch Trials.
The Scorch Trials continues to follow the story of Thomas and other Gladers after The Maze Runner. Fox has hired screenwriter T.S. Nowlin to pen the script.
While the sequel hasn't been greenlit yet, it's not uncommon for a subsequent film's script to be in the works in case the film does well and a sequel wants to be put into production sooner rather than later.
More information at Collider.