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Grain size is an important controlling factor of the chemical composition of sediments. To understand the role of grain size in the content of rare earth elements (REE) in tropical mountainous river sediments and to establish suitable provenance proxies, sediments collected from Pahang River and Kelantan River, Peninsular Malaysia, were determined for REE contents in six size fractions (<2 μm, 2–4 μm, 4–8 μm, 8–16 μm, 16–32 μm, and 32–63 μm). The results indicate that the total REE contents (∑REE) from these two rivers are weakly correlated with grain sizes. The normalized REE patterns of various grain-size fractions to <63 μm fractions revealed a flat pattern for light rare earth elements (LREE), but were gradually enriched in heavy rare earth elements (HREE) with increasing grain size. These results indicate that the grain size constraint on REE is very complex. The relationship between REE contents and mineral compositions of size-fractioned sediments further suggests that clay minerals cause high REE contents in clay components (<2 μm). The dilution effect of quartz and feldspars on REE is another controlling factor, leading to low REE content in medium-fine silt components (2–32 μm). In addition, heavy minerals, zircon, monazite and amphibole, play an important role in enriching REE in coarse silt components (32–63 μm), especially zircon as the major contributor to the enrichment of HREE with increasing grain size. By combining the content of REE, the normalized REE patterns and the REE characteristic parameters for different grain sizes, we find that the 4–8 μm fraction is sensitive to REE variation among the six size fractions investigated. Furthermore, the relationship between upper continental crust-normalized δEu and (Gd/Yb) is reliable for distinguishing the sediment characteristics of Pahang River and Kelantan River and can therefore be used as an effective indicator for identifying Malaysian river-sourced sediments in the southern South China Sea. • REE compositions in different grain-size fractionated sediments from two tropical mountainous rivers are different. • Mineral composition is the main controlling factor of the grain size effect on REE. • The 4–8 μm fraction represents REE variation sensitively among six size fractions investigated in these two rivers. • δEu UCC -(Gd/Yb) UCC discriminant diagram can be used to distinguish Malaysian river-sourced sediments in the southern SCS. [ABSTRACT FROM AUTHOR]