Microplastics (MPs) have been found in the organs of various animals in water environments. However, studies on ingestion and the effects of MPs in fish larvae are still limited. Larval fish of Japanese medaka (Oryzias latipes) were employed to demonstrate ingestion, elimination, and initial effect of MPs after short-term exposure. Three weeks post-hatching (wph) larvae were exposed to fluorescent polystyrene microplastic beads (PS-MPs; diameter 1 μm) for 72 hours (exposure phase), then reared in MP-free freshwater for the next 72 hours (elimination phase). The larvae were sampled at several time points during the experiment. Sampled larvae were fixed, transparentized, and observed under a fluorescent microscope. MPs were detected predominantly in the gastrointestinal tract (GIT). Subsequently, MPs were counted using the fluorescence microscope. MPs were highly ingested during the exposure phase and still detected in the GIT after 72 hours of the elimination phase. Reactive oxygen species (ROS) activity was also measured to examine the initial effect of MP exposure in larvae. ROS levels in larvae that ingested MPs were significantly higher than in non-exposure larvae. These results indicate that MPs remain in GIT for more than 72 hours, and short-term MP exposure can induce ROS activity in O. latipes larvae.