A source separation method using a full-rank spatial covariance model has been proposed by Duong et al. ["Under-determined Reverberant Audio Source Separation Using a Full-rank Spatial Covariance Model," IEEE Trans. ASLP, vol. 18, no. 7, pp. 1830-1840, Sep. 2010], which is referred to as full-rank spatial covariance analysis (FCA) in this paper. Here we propose a fast algorithm for estimating the model parameters of the FCA, which is named Fast-FCA, and applicable to the two-source case. Though quite effective in source separation, the conventional FCA has a major drawback of expensive computation. Indeed, the conventional algorithm for estimating the model parameters of the FCA requires frame-wise matrix inversion and matrix multiplication. Therefore, the conventional FCA may be infeasible in applications with restricted computational resources. In contrast, the proposed FastFCA bypasses matrix inversion and matrix multiplication owing to joint diagonalization based on the generalized eigenvalue problem. Furthermore, the FastFCA is strictly equivalent to the conventional algorithm. An experiment has shown that the FastFCA was over 250 times faster than the conventional algorithm with virtually the same source separation performance.