So far this season, The Thinker’s advantage has been that he can out-think everyone. He knows every variable, every possibility, and every probability. Because of that, he can predict people’s behavior and manipulate them. His plans aren’t perfect—Team Flash finds him sooner than he expected—but he can account for changes and adjust as necessary because he knows everything that’s in play. The Thinker knows everything that could happen but he doesn’t know what will happen for sure.
Barry has a way of knowing what will happen (no time traveling required), and that’s how he can beat The Thinker.
Spoilers for 4×09 “Don’t Run”