Boundary layer transition over an isolated surface roughness element is investigated by means of numerical simulation. Large Eddy Simulation (LES) flow-modeling approach is employed to study flow characteristics and transition phenomenon past a roughness element immersed within an incoming developing boundary layer, at a height-based Reynolds number of 1170. LES numerical results are compared to experimental data from literature showing the time-averaged velocity distribution, the velocity fluctuation statistics and the instantaneous flow topology.Despite slight difference in the intensity of streamwise velocity fluctuations, the present LES results and experimental data show very good agreement. The mean flow visualization shows streamwise counter-rotating vortices pairs formation downstream of the obstacle. The primary pair induces an upwash motion and a momentum deficit that creates a Kelvin-Helmholtz type flow instability. The instantaneous flow topology revealsthe formation of coherent K-H vortices downstream that produce turbulent fluctuations in the wake of the roughness element. These vortices are streched and lifted up when moving downstream. The velocity fluctuations results show that the onset of the turbulence is dominated by the energy transfer of large-scale vortices.