Efficient removal of labile arsenic (As) from paddy soil is a fundamental pathway mitigating As accumulation in rice from a long-term perspective. In this study, a porous and pencil-shaped column prepacked with quartz-supported nanoscale zero-valent iron (NZVI) was designed to extract elevated porewater As from paddy soil under flooded condition. With fine quartz as supporting medium in the core layer, only 0.07% out-migration of the loaded NZVI occurred in arsenite As(III) solution. At pH 5–9, removal of aqueous As(III) with NZVI-column was 73–78%, while silicic acid and phosphate at their environmentally realistic concentrations exhibited 27–30% and 14–17% inhibition on As(III) extraction, respectively. For two paddy soils with slight (S-As) and moderate (M-As) As contamination, four cycles of intermittent extraction with NZVI-column induced steady and marked decrease in porewater As. By the end of four successive extractions, profiles of DGT-labile As in S-As and M-As soils decreased by 22% and 29% on average with simultaneous decline of the most available fraction of soil As (including soluble and exchangeable fraction) by 26% and 17%, respectively. For the post-extracted two soils, As accumulation of rice seedlings declined by 29–57% than those in control. These results identify the effectiveness of NZVI-column in extracting elevated labile As from paddy soils with the aid of flooding. Targeting fast removal of high porewater As, column-extraction could serve as the first step in “remediation train” of paddy soils with relatively high As to shorten cleanup time by rendering much lowered soil As burden for the following phytoextraction and other measures.