Indirubin is the main bioactive component of the traditional Chinese medicine Indigo naturalis and is a bisindole alkaloid. Multiple studies have shown that indirubin exhibits good anticancer, anti-inflammatory and neuroprotective properties. The purpose of this review is to provide a summary of the pharmacological mechanisms of indirubin and its derivatives. Indirubin and its derivatives exert anticancer effects by regulating the expression of cyclin-dependent kinases (CDKs), GSK-3β, Bax, Bcl-2, C-MYC, matrix metalloproteinases (MMPs), and focal adhesion kinase (FAK) through the PI3K/AKT/mTOR, nuclear factor (NF)-κB, mitogen-activated protein kinase (MAPK), JAK/signal transducer and activator of transcription 3 (STAT3) pathways and other signaling pathways. We also reviewed the anti-inflammatory and neuroprotective properties of indirubin and its derivatives. The findings of recent studies assessing indirubin and its derivatives suggest that these compounds can be used as potential drugs to treat tumors, inflammation, neuropathy and bacterial infection. Display omitted •Indirubin is a bisindole alkaloid that is the main bioactive component of the traditional Chinese medicine Indigo naturalis.•Indirubin and its derivatives can exert anticancer effects by regulating multiple signaling pathways.•Indirubin and its derivatives can be used as potential drugs for the treatment of tumors, inflammation, neuropathies and bacterial infections.•This review summarizes the pharmacological mechanisms of indirubin and its derivatives.