The kidney is the primary site of uranium (U) deposition after exposure. The distal portion—S3 segment of the proximal tubules may be involved in U reabsorption from the urine. However, the dynamics of the U distribution in renal tubules have not yet been clearly understood. This study precisely examined the distribution of U within the S3 segment (S3 tubules) in male Wistar rats during the initial phase (1–3 h) of subcutaneous administration with uranyl acetate (UA), 0.5 mg/kg of body weight. X-ray fluorescence spectrometry with a high-energy synchrotron radiation microbeam (SR-μXRF) was employed. At 1 h of administration, U was rapidly transported into the kidneys and accumulated at 4% of the dose. A cross-section of the S3 tubules revealed a distribution of U within the brush border, indicating that U reabsorption was in-progress at this time point. Enhanced U accumulation with a maximum of 134 μg/g was also detected in the epithelium of the S3 tubule microregions. At 3 h, U accumulation in the kidneys was 9%, and U microlocalization in the S3 tubule epithelium reached approximately 200 μg/g. These microlocalization distribution patterns were characteristic of U and differed from those of endogenous trace elements, such as iron and zinc. These findings are valuable for designing decorporation strategies applicable to the U accumulated in this critical organ.