Magnetic circular dichroism (MCD) spectroscopy is a powerful method for evaluating the electronic structure and magnetic and optical properties of molecules. In particular, MCD measurements have been performed on phthalocyanines and porphyrins with various central metal ions, axial ligands, and substituents to elucidate their properties. It is essential to develop a robust high‐throughput technique to perform these measurements comprehensively and efficiently. However, MCD spectroscopy requires very high optical quality for each component of the instrument, and even slight cell distortions can impair the baseline flatness. Consequently, when versatility and data quality are important, an optical system designed for a microplate reader is not suitable for the MCD spectrometer. Therefore, in this study, we develop a new magnetic flow‐through cell and combine it with an existing CD spectrometer and autosampler to construct a high‐throughput system. The effectiveness and performance of this new system are then evaluated. In addition, based on the MCD and absorption spectra of various phthalocyanine complexes, the effects of substituents and solvents on their magnetic and optical properties and the causes of these effects are discussed. The results demonstrate that this system is effective for the evaluation of the physicochemical properties of various phthalocyanine complexes.