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The transparent boundary condition for the free Schrödinger equation on a rectangular computational domain requires implementation of an operator of the form ∂ t − i △ Γ where △ Γ is the Laplace-Beltrami operator. It is known that this operator is nonlocal in time as well as space which poses a significant challenge in developing an efficient numerical method of solution. The computational complexity of the existing methods scale with the number of time-steps which can be attributed to the nonlocal nature of the boundary operator. In this work, we report an effectively local approximation for the boundary operator such that the resulting complexity remains independent of number of time-steps. At the heart of this algorithm is a Padé approximant based rational approximation of certain fractional operators that handles corners of the domain adequately. For the spatial discretization, we use a Legendre-Galerkin spectral method with a new boundary adapted basis which ensures that the resulting linear system is banded. A compatible boundary-lifting procedure is also presented which accommodates the segments as well as the corners on the boundary. The proposed novel scheme can be implemented within the framework of any one-step time marching schemes. In particular, we demonstrate these ideas for two one-step methods, namely, the backward-differentiation formula of order 1 (BDF1) and the trapezoidal rule (TR). For the sake of comparison, we also present a convolution quadrature based scheme conforming to the one-step methods which is computationally expensive but serves as a golden standard. Finally, several numerical tests are presented to demonstrate the effectiveness of our novel method as well as to verify the order of convergence empirically. • We presented an efficient numerical realization of the transparent boundary operator ∂ t − i △ Γ on a rectangular domain. • We first present a convolution quadrature (CQ) based numerical recipe that turns out to be computationally expensive. • A novel Padé algorithm is then developed which removes all bottlenecks of the CQ approach and also of Menza's approach. • A new boundary adapted basis is presented for the spatial problem that ensures the bandedness of the linear systems. • Note that the computational complexity of our novel Padé algorithm remains independent of the number of time-steps. [ABSTRACT FROM AUTHOR]