The present study is concerned with the numerical solution of external boundary conditions in inverse problems for one-dimensional multilayer diffusion, using the difference method. First, we formulate multispecies parabolic problems with three types of Dirichlet–Neumann–Robin internal boundary conditions that apply at the interfaces between adjacent layers. Then, using the symmetry of the diffusion operator, we prove the well-posedness of the direct (forward) problem in which the coefficients, the right-hand side, and the initial and boundary conditions are given. In inverse problems, instead of external boundary conditions of the first and the last layers, point observations of the solution within the entire domain are posed. Rothe’s semi-discretization of differential problems combined with a symmetric exponential finite difference solution for elliptic problems on each time layer is proposed to develop an efficient semi-analytical approach. Next, using special solution decomposition techniques, we numerically solve the inverse problems for the identification of external boundary conditions. Numerical test examples are discussed.