We characterize the role of coherent nanoscale B2 Ni50Al50 precipitates on the temperature- and stress-induced martensitic phase transformation in nanocrystalline Ni63Al37 shape memory alloys using multi-million-atoms molecular dynamics (MD) simulations. We studied two types of precipitates: one with single crystal precipitates (SXP) and a second where grain boundaries cut through precipitates (PXP). Simulations reveal that the presence of B2 precipitates stabilizes the cyclic flag-shaped stress-strain response, characteristic of superelasticity, and reduces remnant strain. In contrast, single-phase nanocrystalline Ni63Al37 exhibits degradation of the reverse transformation during cyclic loading and, eventually, incomplete reversible transformation within a few cycles. This is consistent with previous experimental findings of ultra-low fatigue in Ni-Ti-Cu alloys with Ti2Cu precipitates. The simulations reveal that the presence of precipitates significantly improves the reversibility of the transformation by acting as elastic zones that partially shield the martensitic transformation and drive the reverse transformation. A detailed analysis of the MD trajectories reveals that the martensitic transformation of the matrix induces ultra-large elastic deformation in some of the B2 precipitates (approximately 12%) to the point of resulting in a martensite-like atomic structure.