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We investigate the electron mobility of Si nanowires with 〈100〉, 〈110〉, and 〈111〉 crystalline orientations by considering atomistic electron-phonon interactions. We calculate the electron band structures based on a semiempirical sp3d5s* tight-binding approach and the phonon band structures based on the Keating potential model. Then, by combining the electron and phonon eigenstates based on Fermi’s golden rule and solving the linearized Boltzmann transport equation while considering Pauli’s exclusion principle, we evaluate the electron mobility of Si nanowires. As expected, phonons in Si nanowires are found to behave quite differently from phonons in bulk Si because of phonon confinement. However, electron mobility in Si nanowires is primarily governed by the variation in the electron effective mass rather than that of the phonon eigenstates. As a result, the 〈110〉-oriented Si nanowires showed the highest electron mobility, because they have the smallest electron effective mass among the three orientations.