A numerical simulation of gain measurement performed using the three-antenna method for a log-periodic dipole array antenna (LPDA) is presented. The electromagnetic simulation is based on the finite integration method. The gain variation attributable to measurement distance is estimated when using the conventional method in which the reference point of LPDA is considered. We propose a technique for estimating the phase center by exploiting this gain variation. The simulated results demonstrate the efficacy of considering the phase center for accurate antenna calibration.