We study derived equivalences of certain stacks over genus 1 curves, which arise as connected components of the Picard stack of a genus 1 curve. To this end, we develop a theory of integral transforms for these algebraic stacks. We use this theory to answer the question of when two stacky genus 1 curves are derived equivalent. We use integral transforms and intersection theory on stacks to answer the following questions: if C = P ic d (C), is C = P ic f (C ) for some integer f ? If C = P ic d (C) and C = P ic f (C ), then is C = P ic g (C) for some integer g?