Shikonin and its enantiomeric analogue, alkaninn, are prevailing natural lead compounds in the drug discovery and development of anticancer agents. Despite having numerous biological effects, the most important activity reported for shikonin derivatives is the antitumor effect which is exerted through various mechanisms such as induction of apoptosis and autophagy. The design, synthesis, and development of new shikonin derivatives are continuously performed with the aim of promoting therapeutic effects through increasing cytotoxicity against cancer cells and simultaneously reducing toxicity on normal cells. In spite of significant advances in the development of shikonin derivatives in recent years and the publication of some reviews in this regard, the structural classification, synthesis methods, as well as the diversity of the anti-tumor mechanism of action of these compounds have not been well considered. This review aims to provide comprehensive data in this regard by reviewing studies conducted over the last two decades (from 2000 until now).