We present a resin-packed microchannel that can reduce the radiation exposure risk and secondary radioactive wastes during uranium (U) separation by downscaling the separation using a microchip. Two types of microchips were designed to densely pack the microchannels with resins. The microchannels had almost the same cross-sectional area but different outer circumferences. A satisfactory separation performance could be obtained by arranging more than ca. 10 resins along the depth and width of the microchannels. The resin-packed microchannel is an effective separation technique for determining U concentration via inductively coupled plasma mass spectrometry owing to its ability to avoid the contamination of the equipment by cesium and reduce the matrix effect. The size of the separation site was scaled down to <1/5000 compared to commonly used counterparts. The radiation exposure risk and secondary radioactive wastes can be reduced by 10-and 800-fold, respectively, using the resin-packed microchannel.