Measurement of the heading which is free from magnetic declination by use of several GPS antennas is widely applied, but it is not suitable for small unmanned aerial vehicles because of its limit of the payload and body length. In this paper, we propose a method to estimate the magnetic declination using an IMU and one GPS antenna. The method consists of 1) estimation of the acceleration of the motion from GPS measurements and 2) estimation of the magnetic declination angle using the estimated accelerations and IMU measurements. We show that the estimation of the magnetic declination angle results in reduced QUEST, that is an eigenvalue problem of 2 x 2 real matrix. Experimental results of flight control of an unmanned helicopter demonstrate the effectiveness of the proposed method.