Owing to flooded growing conditions and specific physiological characteristics, rice plant is more efficient in As uptake and accumulation, which provides a cost-effective and time-efficient pathway to deplete bioavailable As from paddy soils. In the present study, the enhancing effect of silicon (Si) fertilization on As extraction from heavily contaminated paddy soils by rice was explored Upon incorporation of one weak acid Si fertilizer (AcSF), soil As solubility was significantly promoted by 1.3–1.4-fold, while a slightly increase in porewater As was observed with alkaline soluble Si fertilizer Na2SiO3 (AlSF). With both Si fertilizers applied before transplanting, a relatively low Si/As molar ratio (<100) in soil porewater was obtained, As a result, soil As uptake by rice plant with Si fertilizers was enhanced by 37.2%–171.7% compared to control (CK). Notably, up to 91.6% of the total As in rice plant retained in root with Si fertilization, suggesting the importance of root removal. By harvesting the whole rice plant including roots, soil bioavailable As measured by diffusive gradients in thin films (DGT) declined by 26.9%–31.3% in AlSF treatments relative to CK. Total soil As depletion by the whole rice plant was significantly enhanced from 2.8% in CK to 7.0%–11.2% in Si fertilizer treatments. In this way, 197.5 mg As m−2-232.5 mg As m−2 could be eliminated from soil following one rice-growth season, which was 2.3–2.7-fold higher compared to CK. These results identified the effectiveness of soluble Si fertilizer in enhancing soil As depletion by rice from paddy soils with high As contamination risk, which could serve as a cost-effective strategy with little technical-restriction.