Determining the starting point of phase in circuit analysis involves understanding that the output phase is relative to the input phase, which can be defined arbitrarily. The phase response can be expressed in forms like theta(jw) = 90 degrees - arctan() or theta(jw) = 0 degrees - arctan(). The choice between using a sine wave or a cosine wave as the input affects the phase shift. Ultimately, the reference point for phase can be set wherever desired, allowing flexibility in analysis. This understanding is crucial for accurate circuit analysis and phase response calculations.