In blood flow through microvessels, platelets are known to be distributed in high concentrations near the vessel wall, termed ‘margination’ or ‘near-wall excess’. At the confluence of two vessels, this preferential distribution of platelets is thought to be compromised and reconstituted in the downstream main vessel. The present study aimed to investigate the distance of this margination reconstruction from the confluence by in vitro experiments using platelet-sized fluorescent particles as a platelet surrogate and a Y-shaped confluence microchannel with rectangular cross sections. Fluorescence microscopy was performed using a confocal laser scanning microscope system to measure the distribution of particles in the red blood cell suspension flow. Immediately after confluence, particles were highly concentrated along a narrow band in the middle of the channel width, where particles located near the inner wall of the daughter channels flowed in. This dense band of particles faded downstream and disappeared less than 5 mm from the confluence. This margination distance is comparable to or smaller than the margination development distance in straight channels, but much smaller than that after bifurcation.