The detection of the primordial B-mode polarization signal of the cosmic microwave background (CMB) would provide evidence for inflation. Yet as has become increasingly clear, the detection of a such a faint signal requires an instrument with both wide frequency coverage to reject foregrounds and excellent control over instrumental systematic effects. Using a polarizing Fourier transform spectrometer (FTS) for CMB observations meets both these requirements. In this work, we present an analysis of instrumental systematic effects in polarizing Fourier transform spectrometers, using the Primordial Inflation Explorer (PIXIE) as a worked example. We analytically solve for the most important systematic effects inherent to the FTS - emissive optical components, misaligned optical components, sampling and phase errors, and spin synchronous effects - and demonstrate that residual systematic error terms after corrections will all be at the sub-nK level, well below the predicted 100 nK B-mode signal.
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