Medicinal plants are the vital source of numerous structurally diverse pharmacologically active metabolites collectively called as secondary metabolites finding extensive applications in traditional systems of medicine and in pharmaceutical industries. Several distinctive and complex pathways operate in an interactive manner via metabolic networks that are responsible for the accumulation of such highly specialized metabolites. Secondary metabolites are believed to play a wide spectrum of physiological and functional roles in plants, many of which being investigated and supported by the experimental studies. Biosynthetic pathway related studies on various aspects in these medicinal plants have been found very tedious owing to several issues in plants such as considerably lower metabolite concentrations in native tissues, existence at different locations, and highly complex multi-step pathways, etc. Pathway elucidation and gene/enzyme discovery for studying metabolic pathway evolution and subsequent engineering could be better achieved by mining various pathway databases and reconstruction of metabolic networks available at different omics databases. Though medicinal plants have a limited range of genomic sequences available, however recently, next generation sequencing is being widely used to generate a comprehensive transcriptomic resource for these plants. It is anticipated that databases and resources generated from these studies are likely to play a key role towards the study and exploitation of metabolites from medicinal plants in near future. In this review, we have discussed next generation sequencing approaches, which were used for the generation of transcriptomic resources for several medicinally important plants. The relevance of transcriptomic approaches in curation of the pathways linked with the synthesis of major secondary metabolites along with their precursors of pharmaceutical importance in medicinal plants is also comprehensively analysed.