In this paper, we study the interaction of roughness induced streaks with pulses of free-stream turbulence towards promoting bypass transition of a laminar boundary layer. A series of eddy resolving simulations are carried out to simulate a transitional boundary layer developing over a flat plate under zero pressure gradient. An isolated roughness element of fixed height is modelled using immersed boundary method and Jarrin’s synthetic eddy method is used to impose free-stream turbulence (FST) at the inlet. We impose pulses of FST to trigger bypass transition in contrast to the continuous forcing typically studied in the literature. For a fixed turbulence intensity and length scale, the pulsing frequency of FST is varied. Interaction between the Klebanoff streaks due to FST with the roughness-induced high and low speed streaks is studied for different pulsing frequencies. Variation in the slope of streamwise evolution of skin friction coefficient is discussed in terms of the relaxation time of the roughness induced streaks which are disturbed when FST pulses pass over it. The dynamics of this interaction and the role it plays in subsequently triggering the bypass transition has been investigated. © 2022, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.