Puerarin is used to treat cardiovascular diseases due to its anti-inflammatory and antifibrotic effects. However, its mechanism of action in atrial fibroblasts is unknown. In this study, we investigated the autophagy pathway and molecular changes in angiotensin II (AngII)-stimulated atrial fibroblasts in response to puerarin treatment. Atrial fibroblasts were cultured and then subjected to stimulation with AngII and puerarin or other chemical drugs (3-MA, CQ, and SP600125). Quantitative real-time polymerase chain reaction and Western blot experiments were used to quantify the expression levels of mRNA and protein. mCherry-GFP-LC3 adenovirus was applied to reflect the autophagic flux. The results showed aggravating levels of autophagy and collagen deposit in the presence of AngII. Puerarin inhibited autophagy and decreased collagen secretion in a dose-dependent manner in atrial fibroblasts. Furthermore, phosphorylation of JNK was down-regulated in response to puerarin, whereas phosphorylation of Akt and mammalian target of rapamycin (mTOR) was upregulated. Interestingly, reduced autophagy and collagen secretion were observed when the JNK signaling pathway was blocked using SP600125. We also observed upregulation of Akt and mTOR phosphorylation in the presence of SP600125. These results suggest that puerarin exerts its antifibrotic effect in atrial fibroblasts partly through the inhibition of autophagy. Furthermore, the mechanism of action of puerarin in fibroblast autophagy seems to be mediated partly through JNK-Akt-mTOR signaling.