The company said Paul Clancy will step down later this year and will be replaced by Aradhana Sarin, the company's current chief strategy and business officer.
Alexion said the transition will happen after the company reports its third-quarter results. Clancy will stay on as a senior adviser until mid-2020.
Alexion CEO Ludwig Hantson said Clancy, who came to the company in July 2017 from Biogen, "played an invaluable role in our efforts to rebuild Alexion, refocus our corporate strategy and position the company for its next chapter."
Dr. Sarin has been with the company since November 2017, is trained as a medical doctor in India, and has more than 20 years of experience at global financial institutions prior to joining Alexion. The company said Dr. Sarin has "extensive knowledge of global healthcare systems as well as an excellent understanding of the biopharmaceutical sector."
Alexion shares were trading down $4.12 to $103.71.