Melissa officinalis (lemon balm) is a medicinal plant producing high-value secondary metabolites that are used in traditional medicine all over the world since the earliest times. Despite pharmacological importance, there is a lack of knowledge about the genes and enzymes involved in secondary metabolite biosynthetic pathways in lemon balm. We identified the key genes and pathways associated with biosynthesis of terpenoid and rosmarinic acid through functional analysis of transcriptomic data. In this study, a comprehensive transcriptome assembly containing 37,055 unigenes was generated by analyzing 42,837,601 Illumina paired-end reads by employing an efficient pipeline. Functional annotation of the unigenes showed that 35,822 (96.67%) and 27,363 (73.84%) had BLAST hits to known proteins in the NR and SwissProt databases, respectively. The KEGG pathway analysis revealed that 10,062 (36.83%) unigenes were assigned to 399 KEGG pathways. The focus of this study was on pathways associated with the production of important metabolites such as terpenes and rosmarinic acid. A total of 149 unigenes were identified that are associated with biosynthesis of terpenoids, including 75 mevalonate and methyl-erythritol phosphate (MEP) pathway genes, terpenoid backbone biosynthesis genes, and 74 terpene synthase genes. Furthermore, 144 and 30 unigenes were detected that are related to the phenylpropanoid biosynthesis and the rosmarinic acid pathway. Therefore, this study lays an accurate and comprehensive transcriptome foundation for future research in the metabolic engineering and identification of novel genes and pathways in lemon balm.