Given two elliptic curves such an isogeny of degree l exists between them, there is an algorithm, due to Elkies, that uses modular equations to compute this isogeny explicitly. It is an essential tool in the SEA point counting algorithm: using isogenies is superior to Schoof's original idea of using endomorphisms. In this work, we present the analogue of Elkies' algorithm for Jacobians of genus 2 curves, thus opening the way to using isogenies in higher genus point counting.