In this study, the effects of boron stress and the application of silicon were investigated on the expression levels of barley homologues of three transporter genes, namely BOR2, PIP1, and PIP1; 1, which have potential in transferring boron and silicon into or out of tissues. Boron toxicity in shoot tissues was observed as early as 1-day-long exposure by means of several stress indicators including ion leakage, malondialdehyde (MDA) and H2O2 levels. Elemental analysis showed that presence of Si under B stress reduces tissue B levels, whereas B presence increased Si levels in tissues. Presence of silicon induced BOR2 gene expression in shoots during early stress. Presence of both elements simultaneously increased BOR2 expression in both shoot and root tissues, which might be attributed to element similarity. Expression levels of both aquaporin genes PIP1 and PIP1; 1 increased in shoots under short term B and Si applications, and levels were more responsive to B when compared to Si. Similar to BOR2 expression, silicon increased both aquaporin gene expressions in shoot tissues under short term boron stress. Investigation of the response of BOR2 and aquaporin genes under boron stress and in the presence of silicon revealed their sensitivity to silicon and their potential function in transporting silicon into tissues. Based on the present work, stress mitigating effects of silicon can be attributed to the competitive role of silicon for the transport via boron transporters under toxic boron levels.