Self-synchronization is a ubiquitous phenomenon in nature, in which oscillators are collectively locked in frequency and phase through mutual interactions. While self-synchronization requires the forced excitation of at least one of the oscillators, we demonstrate that this mechanism spontaneously appears due to activation from thermal fluctuations. By performing molecular dynamics simulations, we demonstrate self-synchronization in a platform supporting doped silicon resonator nanopillars having different eigenfrequencies. We find that pillar's vibrations are spontaneously converging to the same frequency and phase. In addition, the dependencies on the intrinsic frequency difference and the coupling strength agree well with the Kuramoto model predictions. More interestingly, we find that a balance between energy dissipation resulting from phonon-phonon scattering and potential energy between oscillators is reached to maintain synchronization. The balance could be suppressed by increasing the membrane size. While microscopic stochastic motions are known to follow random probability distributions, we finally prove that they can also yield coherent collective motions via self-synchronization.