This work aims to study the two-way shape memory effect degradation due to stress relaxation during holding pre-deformed Ni-50.0 at.% Ti alloy at temperatures from a range of 640–700 K. To initiate the two-way shape memory effect, samples were subjected to 12% preliminary isothermal deformation by torsion in the martensitic state (at room temperature). The influence of holding at 640 or 700 K for 0–60 min on the recoverable strain variation on cooling and heating of the pre-deformed samples was studied. The main degradation of the two-way shape memory effect was found after holding the sample up to 60 min; however, full degradation was not observed, even after holding at 700 K for 6 h. A decrease in the two-way shape memory effect value was believed to be caused by relaxation in the oriented internal stress and it was assumed that this process might be described by a first-order differential equation. This equation was used to simulate the influence of holding duration on the recoverable strain variation and a good correlation between the simulated and experimental data was obtained. The activation energy of the internal stress relaxation during holding at 640 or 700 K was calculated and found to be 0.84 ± 0.01 eV, which was close to the energy of vacancy migration.