Horizontally stratified flows can be seen in a wide variety of micro-scale engineering problems. Recent studies have shown that diffusion at the interface between two liquids leads to a lateral flow, causing the fluid to rotate around the central axis of the channel. This lateral flow has the potential to disrupt the intended mechanism of the device or can be exploited for new device designs. The present investigation presents numerical and experimental results that provide important insights into the effects of the inlet junction on the flow field throughout the microfluidic device. The effects of four different archetypal inlet junctions—an idealized single inlet, counter-flow T junction, perpendicular flow T junction, and Y junction are considered. The results show that counter-flow T junction results in the least amount of lateral flow, while the straight channel results in the highest. The Y channel induces the second least rotation, and the perpendicular T junction creates slightly stronger lateral flows. Furthermore, based on lateral streamlines, it is suggested that the reason for the difference between these junctions can be explained by the interaction of the Dean vortices formed by the rotation of the fluid at the junction and the interaction of the Dean flow with the diffusion-induced vortices. To test this hypothesis, a less common junction (Y junction with angles higher than 180°) is modeled and has shown to reduce the lateral flow even further. Understanding the differences between the junctions would allow for more efficient microfluidic designs for various applications.