Drought is a major environmental factor limiting crop productivity. Considering a significant area of crop production under water-limited rained conditions, there is a great need to develop production systems to sustain yield potentials under drought stress. Silicon has recently been recognized as an important element in plant nutrition. In this study, it was shown that supplying soybean with soluble silicon in the soil could improve vegetative growth and drought tolerance under water limiting conditions. In order to understand the molecular mechanism how silicon alleviates drought stress, the effects of silicon application on protein expression and antioxidant enzymes were examined. Soybean plants were grown in sand-containing pots supplied with 4 millimolar solutions of sodium silicate. To cancel the effect of sodium, the same amount of sodium chloride was used along with control plants. Soluble proteins were isolated from the leaves and roots of silicon-treated and control plants subjected to water deficit stress. Two-dimensional gel electrophoresis and mass spectrometry approaches were used to identify differentially expressed leaf and root proteins in response to silicon application under water deficit stress. Proteins that showed differential expression in response to silicon application included metabolic enzymes and proteins involved in the proteasome-dependent degradation pathway. These results indicate that silicon application could affect enzymes important for carbohydrate metabolism and stabilize aldehyde dehydrogenases and malic enzyme under water deficit stress, which may be attributable to drought tolerance.