Three dimensional dislocation dynamics (DD) simulations are performed to investigate the governing mechanism of size dependent plastic deformation in submicron face-centered cubic (fcc) micropillars under uniaxial loading. Based on previous atomistic simulations, we introduce an algorithm for dislocation nucleation at the free surface as a function of stress and temperature in the DD simulation. The simulation results show stochastic behaviors in agreement with experimental observations, and reveal that dislocation nucleation at the free surface is the dominant mechanism of plastic flow in small pillars with diameters less than 200 nm, while the operation of truncated dislocation sources is the governing mechanism in large pillars with diameters exceeding 1 μm. In between, both mechanisms come into play in a stochastic way.