The distributed parameters of a non-uniform transmission line (NTL) are assumed to depend on a finite set of unknown parameters, for example, their spatial Fourier series coefficients. The line equations are set up taking random voltage and current line loading into account with the random loading being assumed to be white Gaussian noise in the time and spatial variables. Bypassing over to the spatial Fourier series domain, these line stochastic differential equations (SDEs) are expressed as a truncated sequence of coupled stochastic differential equations for the spatial Fourier series components of the line voltage and current. The coefficients that appear in these stochastic differential equations are the spatial Fourier series coefficients of the distributed line parameters and these coefficients in turn are linear functions of the unknown parameters. By separating these complex stochastic differential equations into their real and imaginary part, the line equations become a finite set of SDEs for the extended state defined to be the real and imaginary components of the line voltage and current as well as the parameters on which the distributed parameters depend. The measurement model is assumed to be white Gaussian noise corrupted versions of the line voltage and current sampled at a discrete set of spatial points on the line and this measurement model can be expressed as a linear transformation of the state variables, i.e, of the spatial Fourier series components of the line voltage and current plus a white measurement noise vector. This work uses sparse matrix factorization using Kronecker product to implement the Fourier unitary transform. This work implements perturbation theory for non-uniform transmission line. The extended Kalman filter (EKF) equations are derived for this state and measurement model and our real timeline voltage and current and distributed parameter estimates show excellent agreement with the true values based on MATLAB simulations. The use of sparse matrix factorization using Kronecker product ease the mathematical complexity and provides compact representation.