A Brooklyn brainiac has taken third-place honors — and $50,000 — in the nation’s premier scholastic science contest.

Mimi Yen, 17, a Stuyvesant HS senior from Williamsburg, was the only student from New York to win a top prize at the Intel Science Talent Search, the country’s oldest and most prestigious pre-college science competition.

Yen’s purse comes on top of $7,500 she received as a finalist and $1,000 as a semifinalist.

Her project involves studying worms to learn about circuits in the brain that give clues to human evolution.