Rare earth elements (REEs) from parent materials are easily trapped by secondary minerals in highly weathered soils that contain high pedogenic iron (Fe) oxide levels. However, few studies have investigated REEs fractionation by Fe oxides during pedogenesis. Therefore, this study examined REEs partitioned in the pedogenic Fe oxides of four pedons developed from schist, andesite, shale, and mafic rocks in Eastern Taiwan; this was achieved by combining the dithionite-citrate-bicarbonate (DCB) extraction for bulk soil samples and microspectroscopic approaches for thin sections. The DCB extraction was applied to pedogenic Fe oxides (Fe_d). Furthermore, REE concentrations of the Fe extraction were measured to assess the potential mobility of REEs through the dissolution of pedogenic Fe oxides. The spatial distribution of REEs in Fe nodules and surrounding soil matrix was achieved by using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and electron probe microanalysis (EPMA). The results revealed that total REE content varied with soil depth and among pedons. Total REEs were fractionated during pedogenesis; thus, the ratio of light REEs (LREEs) to heavy REEs (HREEs) varied substantially among all pedons. However, the DCB-extractable REE contents significantly (p < 0.05) increased when the Fe_d contents increased, indicating the high affinity of pedogenic Fe oxides for REEs. Moreover, the pedogenic Fe oxides exhibited an association preference for HREEs over LREEs even though the DCB-extractable concentrations of LREEs were higher than those of HREEs in the soils. Additionally, the association of REEs with Fe oxides led to HREEs condensation in the Fe nodules identified through LA-ICP-MS and EPMA. Our results elucidated pedogenic Fe oxides as the major carrier of REEs while clarifying the preferential trapping of HREEs by pedogenic Fe oxides.