Teenage assassins are a dime a dozen in fantasy and in dystopia, and they aren't ALL that uncommon in historical fiction, but they appear far less often in contemporaries—even stories about teenage spies usually cast the protagonist in an unquestionably heroic role (like Anthony Horowitz's Alex Rider series) or focus on less-problematic skills (like Robin Benway's safe-cracking heroine in Also Known As and Going Rogue).
So, let's look at a few slightly more Questionable Characters!
Four years ago, he learned the truth about his parents, and four years ago, The Program took him in. He was trained physically, mentally, and emotionally, and now he works for them. They give him a target, he infiltrates that target's life, gets close enough, and then moves in for the kill. (Literally.) Then he moves on. Always moving, always alone.
He doesn't know it yet, but this next job will be different.
I Am the Weapon will not be a good fit for every reader: If you dislike the present tense, it won't be a good fit, ditto sentence fragments and antiheroes. Me? It was a GREAT fit.
Benjamin (not his real name) has a voice that is strong and distinct, both emotionally distant and emotionally fragile. He reads like someone who has been programmed, but not entirely brainwashed—he feels trapped in his situation, but hasn't entirely reconciled himself to it; sometimes, he reads like a sociopath, but it's always clear that it's a created state, not a natural one—because he remembers his past, remembers how he came to The Program, he doesn't entirely trust them, isn't entirely in their corner. But he doesn't feel that he has any direction to move in OTHER than theirs, so he falls back on the rules of the game again and again as a way of justifying his actions and of convincing himself to keep moving forward, of not giving up. His keepers see him simply as a tool, as an asset, as a weapon to point at their enemies... but he's more than that: he's a survivor.
Because of his emotional and mental conditioning, because of the way he's lived for the past four years, he doesn't entirely understand human connection—even though he craves it. Although he has been programmed to follow orders, to kill without hesitation or regret or guilt, he remembers the warmth and love he knew as a child, and those memories, in tandem with getting to know his target—not to mention his target's beautiful daughter—are making it more and more difficult for him to perform his duty.
As I read, I found the romance element FAR less interesting and satisfying than in Benjamin's slowly-growing friendship with bullied hacker Howard, but ultimately, Zadoff makes it all work, AND HOW. The sequel is due out in a few weeks (<--Oh, look, it's a Little, Brown title, so Amazon won't let us pre-order it, the jerks), and I'm VERY MUCH looking forward to reading it.
While neither one focuses on a teenage assassin—Miller's is about a pickpocket and Jinks' is about a hacker—and while an argument could be made that they're science fiction OR fantasy OR both, really, I'm including them anyway. They're both about schools for the criminally-minded, and both include characters who're being taught to be assassins. While I was a big fan of both books, I felt that How to Lead a Life of Crime, especially, deserved WAY more attention than it got when it came out.
And here are a couple that I haven't read:
Dear Killer, by Katherine Ewell
This one has been promoted as a story about a teenage girl who happens to be a serial killer, but everything I've read about it suggests that she's actually an assassin with little-to-no conscience. Which is different. Judging by reader reviews at Amazon and GoodReads, response has been EXTREMELY VARIED, so I just ordered a copy so I can make up my own mind.
Boy is forced by his mother to take their Lithuanian exchange student to the prom, it turns out she's an assassin. Hijinks ensue! In the sequel, Perry runs into Gobi in Venice, and there are MOAR HIJINKS. These sound like big, action-movie-esque fun, and I'm going to make a point of reading them soon.
So, I'm sure you've got others to recommend, right? Right?