Medicinal plants have been a source of medicinal compounds and other useful products since ancient times. Due to some limitations, the traditional methods of supplying medicinal compounds are not able to meet the ever-increasing needs of the market, and therefore the use of alternative methods is inevitable. Metabolic engineering is a logical and efficient solution to increase the production of medicinal compounds and reduce related costs. In addition to improving the production of desired metabolites and reducing the production of unwanted metabolites, metabolic engineering also leads to the production of new metabolites in plants. Currently, many methods are used to manipulate metabolic pathways, among which CRISPR/Cas technology has a special place due to its high accuracy and ease of use. In this article, the importance of medicinal plants and their metabolites has been discussed first, and then the necessity of using metabolic engineering to increase the medicinal compounds of these plants has been pointed out. In the following, we have explained the CRISPR/Cas technology and how it works in gene editing. Then, the application of this technology in manipulating the metabolic pathways of medicinal plants is discussed, focusing on three major groups of plant metabolites, namely terpenoids, alkaloids and phenylpropanoids. The next section deals with some of the challenges in the application of this technology in the metabolic engineering of medicinal plants, and proposed solutions. At the end, the future prospects of using this technology in metabolic improvements of medicinal plants are briefly described.