Nobiletin, a polymethoxyflavone widely present in the peel of citrus fruits, has significant anti-inflammatory activity. Autophagy plays a critical role in maintaining cell homeostasis by promoting the degradation of intracellular structures in response to various stress. Recent research suggests the involvement of autophagy in the inflammatory process and therefore some inflammation-related diseases. However, the “cross-talk” between autophagy and nobiletin's anti-inflammation response remains not well elucidated. Therefore, this study was initiated with the aim of investigating the role of autophagy in nobiletin's protective effect against inflammation in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Results showed that nobiletin significantly (P < 0.05) inhibited the release of nitric oxide (NO) and decreased the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in a dose-dependent manner. Moreover, nobiletin significantly (P < 0.05) promoted autophagy as evidenced by the appearance of more autophagosomes, up-regulated LC3II protein, low-regulated p62 protein, and increased autophagy-related (Atg) genes’ expression compared with the control treated with LPS alone. Addition of chloroquine, an autophagy inhibitor, alleviated nobiletin's anti-inflammatory effect, further supporting the requirement of an active autophagy process for the citrus peel flavonoid's biological activity. Mechanistically, we found that nobiletin treatment leads to activation of the IL-6/STAT3/FOXO3a signal pathway through the down-regulation of IL-6 and STAT3 phosphorylation and the upregulation of FOXO3a phosphorylation in the cell nucleus, which is responsible for induction of macrophage autophagy. Taken together, our study provides evidence that nobiletin suppresses inflammatory response through enhancing autophagy through activating the IL-6/STAT3/FOXO3a pathway in macrophage cells.