Isotope labelling of otherwise endogenous metabolites has emerged as a powerful approach to study metabolism-related biological processes, when used in conjunction with nuclear magnetic resonance or chromatography-supported mass spectrometry. Given the advantages of metabolite tracing in uncovering metabolic pathways, there is always a need to develop new methods to generate isotopically labelled compounds. In this direction, we developed a new synthetic route to access the labelled agmatine. To access labelled agmatine, we developed a two-step method that includes the treatment of labelled cyanamide with N-Boc-1,4-butanediamine, followed by a BOC deprotection. Structural confirmation was achieved by 1DNMR, 2DNMR and IR spectroscopy. This isotopologue of agmatine can be very helpful to study the pharmacokinetics and bio-distribution of this neurotransmitter and its metabolites in vitro and in vivo or used as an internal standard in mass spectrometry measurements.