One of the beneficial effects of silicon (Si) is to improve nutrient imbalance including deficiency and excess of nutrients, however the molecular mechanisms underlying this effect are still poorly understood. In this study, we investigated the interaction between Si and zinc (Zn) in rice by using a mutant (lsi1) defective in Si uptake and its wild-type (WT, cv. Oochikara) at different Zn levels. High Zn inhibited the root elongation of both WT and lsi1 mutant, but Si did not alleviate this inhibition in both lines. By contrast, Si supply decreased Zn concentration in both the roots and shoots of the WT, but not in the lsi1 mutant. A short-term (24 h) labeling experiment with stable isotope 67 Zn showed that Si decreased 67 Zn uptake, but did not affect the root-to-shoot translocation and distribution ratio to different organs of 67 Zn in the WT. Furthermore, Si accumulated in the shoots, rather than Si in the external solution, is required for suppressing Zn uptake, but this was not caused by Si-decreased transpiration. A kinetic study showed that Si did not affect K m value of root Zn uptake, but decreased V max value in the WT. Analysis of genes related with Zn transport showed that among ZIP family genes, the expression of only OsZIP1 implicated in Zn uptake, was down-regulated by Si in the WT, but not in the lsi1 mutant. These results indicate that Si accumulated in the shoots suppresses the Zn uptake through down-regulating the transporter gene involved in Zn uptake in rice.