Gain independent reference channel measurement system and method. A method of making robust, stable measurements, in a variety of different applications is disclosed. More specifically, this disclosure describes systems and methods relating to performing gain independent reference channel measurements by making two phase measurements of a device under test. Mathematically, the measurements are combined and many common mode parameters drop out. The result yields an analysis of a device under test analysis which mitigated errors, predominately arising from environmental variations and changes in circuit behavior stemming from swings in signal input.