There are a large number of pharmaceutical products in the market containing heterocyclic compounds. Heterocyclic compounds are explored in the field of therapeutics due to their unique physicochemical and pharmacological properties. A large number of heterocyclic compounds existing in the pharmaceutical market have marked anticancer activity and many of them are under research investigations to treat different types of cancers. Anticancer heterocyclic compounds show many shortcomings such as other anticancer agents in bioavailability and site-specific drug delivery resulting in toxicity and decreased patient compliance. These shortcomings can be eliminated by applying the principles of nanotechnology. The present review discloses the biochemical mechanism of action, different biological targets, intrinsic shortcomings, and structure-activity relationships of anticancer heterocyclic compounds. Furthermore, the role of different nanocarrier systems in selective biological targeting and alteration of pharmacokinetic and pharmacodynamic characteristics of anticancer heterocyclic compounds will be discussed in detail.