Electrical runout (ERO) reflects the heterogeneity of electromagnetic characteristics on surface of shaft. On-site measurement can inspect whether the ERO satisfies the processing and the machine operating requirements. It is very important for controlling the product quality and ensuring the working property. An on-site measurement technology of ERO on shaft based on eddy current was presented. Firstly, the working principle of eddy current sensor and the distribution of eddy were introduced. Then, a finite element analytical model for measuring ERO was developed. Finally, an on-site measurement system was set up to measure the ERO of air compressor main shaft. The results verify the validity of measurement system.