The estimation of the equivalent current distribution is a challenge when the precise geometry of the real source is unknown. In this study, a novel estimation method for the equivalent current distribution is proposed. The proposed method is a hybrid of the Fourier transform and eigenmode currents of equivalent sources. The equivalent current distribution is estimated using the proposed method as follows. First, the Fourier transform is applied to an electric field integral equation, and the initial equivalent current distribution on a specific estimation plane is estimated from the near-field data of the real source. Utilizing the initial equivalent current distribution, the equivalent sources that are uniformly arranged over the estimation plane are thinned. Subsequently, the equivalent current distribution is estimated using a matrix equation and the eigenmode currents of the remaining equivalent sources. The advantages of the proposed method are as follows. First, the precise geometry of the real source is not needed during estimation. Second, the number of equivalent sources is reduced, and the estimation of the equivalent current distribution is well conditioned. The performance of the proposed method is validated both numerically and experimentally. Empirical guidelines for threshold values for thinning equivalent sources are provided.