Abstract: Improving signal-to-noise and analyte resolution are perpetual analytical challenges for capillary electrophoresis (CE) detection methods. Fourier transform-based techniques have been developed to address these challenges including Shah Convolution Fourier Transform (SCOFT), two-beam fluorescence cross-correlation, Hadamard Transform CE, and Fourier Transform CE (FT-CE). This work proposes a new FT-CE approach utilizing a single capillary and a linear array of 3D printed fluorescence detection heads placed at equally spaced locations along the capillary. The detector array is fiber coupled to a single photomultiplier tube (PMT) transducer, generating a complex time-domain signal suitable for Fourier analysis to produce a frequency domain electropherogram. Each 3D printed detection head integrates two independent optical paths, one for spectral and spatial filtering of excitation light and an orthogonal path for capturing emission and coupling to an optical fiber for transmission to the PMT. The operating principle is similar to SCOFT, however, dedicated optical paths at each detection point improve the efficiency of collecting emitted light compared to wide-area imaging. The design and operation of a single detection head is reported, and the incorporation of this detector into a commercial CE-instrument is described. Detection limits of 0.92 ± 0.2 nM have been achieved for separation of fluorescein in borate buffer (pH 8). Optimization of device geometry, excitation intensity, and detector gain are discussed. Multiphysics simulations and preliminary experiments of FT-CE detection will be presented.