Abstract Arachidonate 5‐lipoxygenase (ALOX5) expression and activity has been implicated in tumor pathogenesis, yet its role in papillary thyroid carcinoma (PTC) has not been characterized. ALOX5 protein and mRNA were upregulated in PTC compared to matched, normal thyroid tissue, and ALOX5 expression correlated with invasive tumor histopathology. Evidence suggests that PTC invasion is mediated through the induction of matrix metalloproteinases (MMPs) that can degrade and remodel the extracellular matrix (ECM). A correlation between MMP‐9 and ALOX5 protein expression was established by immunohistochemical analysis of PTC and normal thyroid tissues using a tissue array. Transfection of ALOX5 into a PTC cell line (BCPAP) increased MMP‐9 secretion and cell invasion across an ECM barrier. The ALOX5 product, 5(S)‐hydroxyeicosatetraenoic acid also increased MMP‐9 protein expression by BCPAP in a dose‐dependent manner. Inhibitors of MMP‐9 and ALOX5 reversed ALOX5‐enhanced invasion. Here we describe a new role for ALOX5 as a mediator of invasion via MMP‐9 induction; this ALOX5/MMP9 pathway represents a new avenue in the search for functional biomarkers and/or potential therapeutic targets for aggressive PTC. J. Cell. Biochem. 113: 1998–2008, 2012. © 2012 Wiley Periodicals, Inc.