Microelectromechanical systems (MEMS) are increasingly playing a significant role in the aviation industry and space exploration. Moreover, there is a need to study the neutron radiation effect on the MEMS structural members and the MEMS devices reliability in general. Experiments with MEMS structural members showed changes in their operation after exposure to neutron radiation. In this study, the neutron irradiation effect on the flexible MEMS resonators’ stability in the form of shallow rectangular shells is investigated. The theory of flexible rectangular shallow shells under the influence of both neutron irradiation and temperature field is developed. It consists of three components. First, the theory of flexible rectangular shallow shells under neutron radiation in temperature field was considered based on the Kirchhoff hypothesis and energetic Hamilton principle. Second, the theory of plasticity relaxation and cyclic loading were taken into account. Third, the Birger method of variable parameters was employed. The derived mathematical model was solved using both the finite difference method and the Bubnov–Galerkin method of higher approximations. It was established based on a few numeric examples that the irradiation direction of the MEMS structural members significantly affects the magnitude and shape of the plastic deformations’ distribution, as well as the forces magnitude in the shell middle surface, although qualitatively with the same deflection the diagrams of the main investigated functions were similar.