We introduce the frequency transfer function (FTF) formalism for generalized least squares phase-shifting algorithms (GLS-PSAs), whose phase shifts are nonuniformly spaced. The GLS-PSA’s impulsive response is found by computing the Moore–Penrose pseudoinverse. FTF theory allows analyzing these GLS-PSAs spectrally, as well as easily finding figures of merit such as signal-to-noise ratio (SNR) and harmonic rejection capabilities. We show simulations depicting that the SNR slightly decreases as the harmonic rejection robustness improves.