In 2020, Stoffels "spearheaded the development of the Johnson & Johnson single-shot Covid-19 vaccine within a record time frame," the company said.
The executive, 59, also led the transformation of the research-and-development pipeline for the Janssen Pharmaceutical unit.
Stoffels, who also is vice chairman of the board's executive committee, is retiring to spend more time with his family in Europe and to cut down on travel, The Wall Street Journal reported, citing an unnamed source. He frequently flew back and forth between the U.S. and Europe for work.
He played a key role in many collaborations with external partners including the licensing of key medicines, as well the acquisition of Crucell and Actelion.
Stoffels "generated a huge impact on global health and on the trajectory of Johnson & Johnson,” Chairman and Chief Executive Alex Gorsky said in a statement.
In August, the company said Gorsky would step down later this year. J&J tapped industry veteran Joaquin Duato as his successor.
Gorsky, who has led the group since 2012, will become executive chairman on Jan. 3. He cited "family health reasons" for what was a surprise decision to leave the CEO's post.
Duato, 59, will take over as CEO, capping a three-decade career with the group. His tenure has included stints leading the consumer products division and overseeing its technology and supply-chain operations.
Shares of the New Brunswick, N.J., company, at last check edged lower 0.4% to $159.62.