Perhaps the most prominent theme of this book, and one that is alluded to in the title The Innocent Man, is the exploration of what happens when the American criminal justice system does not function as it is supposed to. While the trials of Ron Williamson and Dennis Fritz are the main focus of the book, Grisham draws on numerous other accounts of justice gone wrong to show that situations in which innocent people are put in jail, or even executed, for crimes they did not commit, are more common than one might think. Grisham himself admits in the epilogue that this particular case opened his eyes to the true costs of wrongful conviction.

In this book, miscarriage of justice is portrayed as predominantly an individual issue, rather than the result of systemic issues or biases. "Ada is a nice town," writes Grisham, "and the obvious question is: When will the good guys clean house?" (214). There is an underlying assumption that if certain people in positions of authority were driven by a real desire to find the truth, rather than their egos and their pride, the justice system would function as it is designed to do, and innocent men would not go to jail.