Magnetic circularly polarized luminescence (MCPL) spectroscopy is widely used to evaluate the luminescence dissymmetry factor (gMCPL) for compounds. However, even for the same instrument and operating conditions, the measured gMCPL is affected by errors associated with sources such as baseline drift and spectral noise, and so the range of variation of gMCPL must be considered when comparing values, which requires multiple measurements for the same sample. Also, because many samples undergo photodegradation under excitation light, it is difficult to accumulate and average spectra for samples with weak MCPL signals to improve the signal‐to‐noise ratio. Single measurements must therefore be performed on multiple samples and the results averaged. Furthermore, for samples with a small Stokes shift, spectral correction is required to compensate for the intensity reduction due to the inner‐filter effect (IFE). Such measurements are generally performed manually and are therefore time consuming and prone to human error. Here, we demonstrate the use of a newly developed high‐throughput MCPL system to automatically measure MCPL and fluorescence spectra of multiple samples of phthalocyanine complexes with high efficiency and reduced human errors. This system allows the incorporation of effective countermeasures to the issues of gMCPL variation, sample photodegradation, extremely weak MCPL signals, and the IFE.