Little Brother has major themes that, according to some, are too serious for a young adult novel. In an interview, the Journal of Adolescent & Adult Literacy asked Doctorow about his "potentially heavy themes, including paranoia, loyalty, sex, torture, [and] fear" and when his editing staff asked to censor the themes. He replied, "Oh, no."
The Hollywood Reporter remarked, "The book tackles many themes, including civil liberties and social activism".
According to journalist April Spisak's article on "What Makes a Good Young Adult Dystopian Novel?" Spisak claims, "Cory Doctorow’s Little Brother probably represents the purest example on the list—modern technology meets classic dystopic elements—even while the book itself is part instructional guide, part love story, and part rant at the increasingly dictatorial powers that be that consider safety at any cost a reasonable exchange. Small personal victories for the protagonist and his friends are present, but the power of Big Brother is hardly tempered by their work, and the folks who tangled with the government are all permanently scarred by the encounter."
The book has also been stated as "[expressing] astonishment, fear, uncertainty, shame, and guilt" and shows "issues of political authority, social order, individual freedom and electronic security."