Microwave Kinetic Inductance Detectors (MKIDs) are photon detectors comprised of superconducting LC resonators with unique resonant frequencies corresponding to their geometrical structure. As each pixel has its own geometry, electromagnetic simulations by hand of every pixel in a kilo-pixel array are impractical. Simulating fewer pixels and interpolating in between risks reduced pixel yield in arrays due to overlapping resonant frequencies. We introduce a new software called AEM (Automated Electromagnetic MKID simulations) that automates the construction and simulation of every simulated MKID pixel in an array according to specified resonant frequencies and a Q c range. We show automated designs to have an increased pixel yield (avoiding loses due to interpolation completely), increased accuracy in resonance frequency and Q c values when compared to interpolated structures. We also demonstrate a simulated trial of AEM for 100 MKIDs between 4 and 8 GHz to produce MKIDs with accuracies of ± 0.2 MHz with a runtime of 10 h 45 min.