The root of Scutellaria baicalensis (Scutellaria Radix) is a medicinal part being used as a herbal drug; while its stem and leaf (aerial part) are considered as waste. Several reports have shown that aerial part of S. baicalensis (SBA) has chemical similarity with its root, suggesting the possible usage of this non-medicinal part. Thus, the usage of SBA as an additive in aquaculture feeding could be a new way to recycle the waste. The water extract of SBA inhibited the growth of several common pathogenic bacteria in aquaculture, e.g. Aeromonas hydrophila, Edwardsiella tarda, Vibrio alginolyticus and Vibrio harveyi. In cultured macrophage cells (RAW 264.7), application of SBA extract showed strong anti-inflammation effect, which inhibited the expression of inflammatory cytokine, i.e. IL-1β, as induced by LPS. Similarly, SBA extract suppressed the LPS-induced transcriptional activity mediated by NF-κB. When applied in fish aquaculture, the extract of SBA was mixed into the feedings of Siganus fuscescens (rabbit fish) that was cultured with a mixture of pathogenic bacteria. The expression levels of COX-2, IL-1β and TNF-α were markedly reduced in the present of SBA extract. Our investigations show the anti-bacterial effect of SBA extract, as well as its potential anti-inflammation effects both in vitro and in vivo, which therefore suggest the possible development of S. baicalensis aerial part in fish aquaculture.