Post-transcriptional modifications of RNA diversify the genetically encoded sequences and play important roles in fundamental cellular processes like mRNA and rRNA maturation. Most RNA methylations are catalyzed by S-adenosylmethionine-dependent RNA methyltransferases. An assay for rapid and easy detection of this enzymatic activity would be highly desirable to identify novel RNA methyltransferases, test S-adenosylmethionine analogs or screen RNA methyltransferase inhibitors. We have developed an enzyme-coupled assay to determine the activity of trimethylguanosine synthases, a class of RNA methyltransferases responsible for RNA cap hypermethylation in eukaryotes. We show that this assay can be used in E. coli cell lysate to measure the activity of recombinantly produced trimethylguanosine synthase. Potential hits are validated for formation of hypermethylated product using HPLC and MALDI-TOF-MS. Furthermore, we demonstrate how this assay can be implemented to screen methyltransferase inhibitors.