Junction flow occurs at a blockage in flow over a surface, where the area upstream of the blockage experiences increased turbulence and heat flux due to flow separation and reattachment of the approach boundary layer. This phenomenon is common in turbine blades and submarine appendages. The flow commonly develops into a horseshoe vortex that drives freestream fluid into the endwall, enhancing local heat transfer. The horseshoe vortex is highly unsteady for a junction with a turbulent approach boundary layer, where the unsteadiness is thought to be linked to the frequency of incoming turbulent structures. In previous studies, the presence of high freestream turbulence in a constant approach velocity showed increased heat flux in the junction region due to increased unsteadiness of the junction flow. Junction flows can also experience periodic variation in freestream velocity, especially in turbomachinery, yet no studies have examined how the junction flow unsteadiness might be affected by this. This paper investigates the effect of pulsing the freestream flow in front of a symmetric research airfoil geometry. The pulsing flow is generated by a variable tunnel blockage that can be controlled to various speeds. Time-average heat flux in the presence of various freestream velocity variations indicate useful findings considering heat transfer coefficient, centerline Stanton number, and Stanton number augmentation.