We study the inverse scattering problem for a Schrödinger operator related to a static wave operator with variable velocity, using the GLM (Gelfand–Levitan–Marchenko) integral equation. We assume to have noisy scattering data, and we derive a stability estimate for the error of the solution of the GLM integral equation by showing the invertibility of the GLM operator between suitable function spaces. To regularise the problem, we formulate a variational total least squares problem, and we show that, under certain regularity assumptions, the optimisation problem admits minimisers. Finally, we compute numerically the regularised solution of the GLM equation using the total least squares method in a discrete sense.