In this paper, we use evolutionary algorithm to evolve customized quantum key distribution (QKD) protocols designed to counter attacks against the system in order to optimize the speed of the secure communication. This is in contrast to most work in QKD protocols, where a fixed protocol is designed and then its security is analyzed to determine how strong an attack it can withstand. We show that our system is able to find protocols that can operate securely against attacks where ordinary QKD protocols would fail. Our algorithm evolves protocols as quantum circuits, thus making the end result potentially easier to implement in practice.