Microplastic (MP) pollution and the related impacts on aquatic species have drawn worldwide attention. However, knowledge of the kinetic profiles of MPs in fish remains fragmentary. In this study, we conducted exposure and depuration tests of the following fluorescent-labeled MPs: polyethylene (PE; sphere with 200 or 20 µm diameter) and polystyrene (PS; sphere with 20 or 2 µm diameter) using juvenile Japanese medaka (Oryzias latipes). The distribution and concentration of MPs in medaka were directly determined in-situ after tissue transparency. During the 14-day exposure, MPs was mainly detected in the gastrointestinal tract, while some MPs at the size of ≤ 20 µm were located in the area of the gills and head. The bioconcentration factor (BCF; L/kg) for MPs in medaka was estimated as 74.4 (200 µm PE), 25.7 (20 µm PE), 16.8 (20 µm PS), and 139.9 (2 µm PS). Within the first five days of depuration, MPs were exponentially eliminated from the fish body, but 2 µm PS-MPs could be still detected in the gastrointestinal tract at the end of the 10-day depuration phase. Our results suggest that MPs 2 µm in diameter may pose ecological risks to aquatic species due to their relatively higher BCF and the potential for long-term persistence in the body.