We present an automated procedure for the design of optimal actuation for flagellar magnetic microswimmers based on numerical optimization. Using this method, a new magnetic actuation method is provided which allows these devices to swim significantly faster compared to the usual sinusoidal actuation. This leads to a novel swimming strategy which makes the swimmer perform a 3D figure-8 trajectory. This shows that a faster propulsion is obtained when the swimmer is allowed to go out-of-plane. This approach is experimentally validated on a scaled-up flexible swimmer.