A linear boundary value problem for essentially loaded differential equations is considered. Using the properties of essentially loaded differential we reduce the considering problem to a two-point boundary value problem for loaded differential equations. This problem is investigated by parameterization method. We offer algorithm for solving to boundary value problem for the system of loaded differential equations. This algorithm includes of the numerical solving of the Cauchy problems for system of the ordinary differential equations and solving of the linear system of algebraic equations. For numerical solving of the Cauchy problem we apply the Runge–Kutta method of 4th order. The proposed numerical implementation is illustrated by example.