A new scheme for the automated design and optimization of electromagnetic energy harvesters is presented. The proposed method aims to deal with the limitations of current design techniques and to improve the efficiency of the design process. Most of the current design approaches require significant user experience and knowledge to make informed design decisions, which means that a large amount of time is needed to obtain the optimized design. Additionally, the design solution is suitable only for a specific application, which makes it difficult to adopt it to other application demands. In the proposed method, the development cycle has been sped up significantly by minimizing human efforts and utilizing a generic model for the design process. The method is based on a generic template based on specific resources and requirements, which is processed by a black-box optimization algorithm to come up with a number of promising configuration suggestions. The method's effectiveness and its autonomous operation are demonstrated based on the design optimization of an electromagnetic pick-up unit for vibration energy harvesters using a Halbach array.