Eddy current testing is a widely used technique for electrical conductivity measurement due to its advantage of contactless measurement. However, the results are easily influenced by liftoff change. In this study, a new solution to compensate for the liftoff effect in eddy current measurements of conductivity is proposed. By measuring the inductance of coils with different frequencies, the liftoff–conductivity solution sets at each frequency are obtained from an analytical model. By finding a common solution for all frequencies, we can obtain the liftoff of the probe and the conductivity of the specimen simultaneously, thus improving the accuracy and reliability of conductivity measurements. For a liftoff variation of 1.14 mm, the introduced measurement error is up to 70.46% for aluminum alloys without liftoff compensation. By finding the common solution for multiple frequencies, the error is reduced to less than 5.57%. The selection of the frequency and tolerance limit is also discussed for the proposed method.