Autophagy inhibition is an attractive target for cancer therapy. In this study, we discovered inhibitors of Atg4B essential for autophagosome formation and evaluated their potential as therapeutics for prostate cancer. Seventeen compounds were identified as candidates after <i>in silico</i> screening and a thermal shift assay. Among them, compound <b>17</b> showed the most potent Atg4B inhibitory activity, inhibited autophagy induced by anti-castration-resistant prostate cancer (CRPC) drugs, and significantly enhanced apoptosis. Although <b>17</b> has been known as a phospholipase A<sub>2</sub> (PLA<sub>2</sub>) inhibitor, other PLA<sub>2</sub> inhibitors had no effect on Atg4B and autophagy. We then performed structural optimization based on molecular modeling and succeeded in developing <b>21f</b> (by shortening the alkyl chain of <b>17</b>), which was a potent competitive inhibitor for Atg4B (<i>K</i><sub>i</sub> = 3.1 μM) with declining PLA<sub>2</sub> inhibitory potency. Compound <b>21f</b> enhanced the anticancer activity of anti-CRPC drugs <i>via</i> autophagy inhibition. These findings suggest that <b>21f</b> can be used as an adjuvant drug for therapy with anti-CRPC drugs.