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A deep study of the metabolic content of the tunicate <i>Polycarpa aurata</i>, collected from Indonesian coast, afforded the isolation of two novel alkaloids, polyaurines A (<b>1</b>) and B (<b>2</b>), along with two new <i>p</i>-substituted benzoyl derivatives (<b>3</b> and <b>4</b>) and four known compounds (<b>5</b>&#8722;<b>8</b>). The structural elucidation of the new secondary metabolites was assigned by 1D, 2D NMR, and HRESIMS techniques. Computational studies resulted a useful tool to unambiguously determine in polyaurine B the presence of rarely found 1,2,4-thiadiazole ring. The effects of polyaurines A and B on mammalian cells growth and on the viability of different blood-dwelling <i>Schistosoma mansoni</i> (phylum: Platyhelminthes) stages, as well as egg production, were evaluated. Both compounds resulted not cytotoxic; interestingly some of the eggs produced by polyaurine A-treated adult pairs in vitro are smaller, deformed, and/or fragmented; therefore, polyaurine A could represent an interesting bioactive natural molecule to be further investigated.