We previously reported on the use of fast cyclic square wave voltammetry (FCSWV) as a new voltammetric technique. Fourier transform electrochemical impedance spectroscopy (FTEIS) has recently been utilized to provide information that enables a detailed analytical description of an electrified interface. In this study, we report on attempts to combine FTEIS with FCSWV (FTEIS-FCSWV) and demonstrate the feasibility of FTEIS-FCSWV in the in vivo detection of neurotransmitters, thus giving a new type of electrochemical impedance information such as biofouling on the electrode surface. From FTEIS-FCSWV, three new equivalent circuit element voltammograms, consisting of charge-transfer resistance (Rct), solution-resistance (Rs), and double-layer capacitance (Cdl) voltammograms were constructed and investigated in the phasic changes in dopamine (DA) concentrations. As a result, all Rct, Rs, and Cdl voltammograms showed different DA redox patterns and linear trends for the DA concentration (R2 > 0.99). Furthermore, the Rct voltammogram in FTEIS-FCSWV showed lower limit of detection (21.6 ± 15.8 nM) than FSCV (35.8 ± 17.4 nM). FTEIS-FCSWV also showed significantly lower prediction errors than FSCV in selectivity evaluations of unknown mixtures of catecholamines. Finally, Cdl from FTEIS-FCSWV showed a significant relationship with fouling effect on the electrode surface by showing decreased DA sensitivity in both flow injection analysis experiment (r = 0.986) and in vivo experiments. Overall, this study demonstrates the feasibility of FTEIS-FCSWV, which could offer a new type of neurochemical spectroscopic information concerning electrochemical monitoring of neurotransmitters in the brain, and the ability to estimate the degree of sensitivity loss caused by biofouling on the electrode surface.