A method has been developed for the synthesis of two isotopically labelled forms of a pro‐drug of the acetylcholinesterase inhibitor (−)‐huperzine A. These labelled compounds,[14C]ZT‐1 (Debio‐9902) and [d3]ZT‐1, were used in clinical studies to evaluate a potential treatment for Alzheimer's disease. The pro‐drug [14C]ZT‐1 was isolated with a radiochemical purity of >98% and a gravimetric specific activity of 129 μCi/mg in a seven‐step synthesis starting from [U‐14C]phenol in 7% yield. Subsequently, the deuterium labelled target (−)‐[d3]huperzine A was achieved in six steps with an overall yield of 15% and gave an isotopic distribution of d2 (1.65% huperzine A) and d3 (97.93% huperzine A) with a chemical purity of 98.5%. Condensation of the substrate (−)‐[d3]huperzine A with 5‐chloro‐o‐vanillin gave the Schiff base [d3]ZT‐1 in a chemical yield of 80%. Reduction of the Schiff base gave reduced‐[d3]ZT‐1, which was converted into the hydrochloride salt with an isotopic distribution of d2 (1.60%) and d3 (98.02%). Copyright © 2011 John Wiley & Sons, Ltd.