The inverse problem of recovery of a potential on a quantum tree graph from the Weyl matrix given at a number of points is considered. A method for its numerical solution is proposed. The overall approach is based on the leaf peeling method combined with Neumann series of Bessel functions (NSBF) representations for solutions of Sturm–Liouville equations. In each step, the solution of the arising inverse problems reduces to dealing with the NSBF coefficients. The leaf peeling method allows one to localize the general inverse problem to local problems on sheaves, while the approach based on the NSBF representations leads to splitting the local problems into two‐spectrum inverse problems on separate edges and reduces them to systems of linear algebraic equations for the NSBF coefficients. Moreover, the potential on each edge is recovered from the very first NSBF coefficient. The proposed method leads to an efficient numerical algorithm that is illustrated by numerical tests.