Eddy current spectroscopy is capable of mapping conductivities and thicknesses of layered structures due to its frequency-dependent penetration depth. High-frequency apparent eddy current conductivity (AECC) spectroscopy applications typically mandate covering a frequency range beyond 10 MHz to capture depth-dependent conductivity profiles. Following the standard four-point linear system calibration method beyond 10 MHz makes it difficult to achieve accurate AECC measurements due to spurious self- and stray-capacitive effects where complex eddy current coil impedance variation with lift-off becomes more nonlinear. In this study, two different approaches are presented to reduce AECC measurement sensitivity to lift-off. First, a nonlinear lift-off correction is developed as a function of measured apparent eddy current lift-off. Second, a semi-quadratic system calibration is developed to capture the lift-off curvature as a function of frequency and hence minimizes the measurement sensitivity to lift-off variations. Presented calibration techniques allow more robust AECC measurements up to 80–100 MHz with one-order of magnitude improvement in accuracy in comparison to the use of standard four-point linear system calibration in a lift-off range of ±25.4 µm.