Studying chemical reactions, particularly in the gas phase, relies heavily on computing scattering matrix elements. These elements are essential for characterizing molecular reactions and accurately determining reaction probabilities. However, the intricate nature of quantum interactions poses challenges, necessitating the use of advanced mathematical models and computational approaches to tackle the inherent complexities. In this study, we develop and apply a quantum computing algorithm for the calculation of scattering matrix elements. In our approach, we employ the time-dependent method based on the Møller operator formulation where the S-matrix element between the respective reactant and product channels is determined through the time correlation function of the reactant and product Møller wavepackets. We successfully apply our quantum algorithm to calculate scattering matrix elements for 1D semi-infinite square well potential and on the colinear hydrogen exchange reaction. As we navigate the complexities of quantum interactions, this quantum algorithm is general and emerges as a promising avenue, shedding light on new possibilities for simulating chemical reactions on quantum computers.