With the breakthroughs made by physicists in high‐dimensional mathematics, it has become possible to represent and solve a number of classical mathematical physics problems using the split quaternion algebra. In this paper, we study the least squares approximation of a class of Schrödinger equations in split quaternionic mechanics and propose two algebraic algorithms to the generalized right eigen‐problem for an i‐Hermitian split quaternion matrix pencil by using two isomorphic mappings. Numerical examples show the effectiveness of the proposed theories and algorithms.