The Joker knows Batman's secret identity – and, weirdly, a Punisher/Batman crossover best explains how he figured it out. The Joker has always been Batman's most terrifying opponent, a relentless force of anarchy and chaos who revels in the mayhem he leaves in his wake. But the threat of the Joker recently became worse than ever before, when he revealed he has long known Batman is really Bruce Wayne.
Apparently, the Joker has known Batman's secret identity for years, but he never really wanted to take advantage of the knowledge. Doing so would change the game in Gotham far too much, spoiling the fun. But then Superman revealed his secret identity to the world, and the Joker feared his cowled nemesis would follow suit. And so the Joker initiated his endgame plan, wreaking havoc on a scale never seen before in the epic "Joker War." The Joker even stole the Wayne fortune, using it to fund his own nefarious activities. But even as the Joker came closer to defeating Batman than ever before, even as the entire Bat-family reeled upon learning that the Joker had figured out who they all were, one question remained: just how did the Joker discover Bruce Wayne was Batman?
Bizarrely, the most likely answer is provided in the Punisher/Batman: Deadly Knights one-shot by Chuck Dixon and John Romita Jr., published back in 1994. This saw the Punisher head to Gotham in pursuit of his own nemesis Jigsaw, only to learn his enemy had formed an alliance with the Joker. Needless to say, Bruce didn't take kindly to learning Frank Castle was in town, but the two were soon forced to work together. The plot took a twist when each hero wound up facing the other's traditional opponent, with the Joker horrified at an enemy who really would kill him if he got the chance. Even as he fled, though, the Joker couldn't resist taunting the Punisher.
"Jiggy told me your whole sad story," the Joker babbled as he ran for his life. "Your family got themselves killed. So sad. Y'know, I think something similar happened to Batty. But it happened a long time ago. Do you know how I know that?" The Joker's words achieved their objective, distracting the Punisher long enough for the Joker to blind him with a muzzle flash from a gun, but of course, he carried on talking all the same. "The masquerade," the Joker explained. "The gadgets. He reacted just as a child would." The Clown Prince of Crime has correctly realized Batman's quest is not for justice, but rather for control; it is a child's cry of pain as he lost the ability to control his own fate.
It's not hard to see how this deduction would lead to the Joker's realizing just who Batman really is. After all, those gadgets require a lot of money to pay for them, and Bruce Wayne is the most famous wealthy citizen of Gotham to have lost his parents to crime when he was just a child. It seems the Joker is every bit as good a detective as Batman himself – and his deductive powers led him to figure out the Caped Crusader's true identity. Of course, he couldn't help but blab all of that to Punisher.