This article describes a systematic approach to decoupling automatic tuning control (ATC) and automatic matching control (AMC) systems in continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy for animal experiments. This technique enables us to improve the stability of CW-EPR spectroscopy even if the animal is moving during the data acquisition of EPR spectra. The control systems are formulated to allow the behavior of interference between them to be investigated, since they are generally coupled due to the characteristics of the microwave resonator. The stability of the entire control system in a 1.1 GHz CW-EPR spectrometer is evaluated with the generalized Nyquist stability criterion. We compare the EPR spectra of a triarylmethyl (TAM) radical that is dosed in anesthetized mice in terms of the signal-to-noise ratio (SNR) to test the precompensator for decoupling the ATC and AMC systems. The experimental findings suggest that the present technique is useful for improving the SNR of EPR spectra in animal experiments. The SNR of the measured EPR spectra was improved by about 50% with the precompensator.