Biogen was formed as an international biotechnology company in 1978, on the initiative of the venture capital department of Inco (International Nickel Company of Canada). Its purpose was to exploit the commercial potential of advanced microbiological science, principally DNA recombinant technology and advanced mutational technology.

The company was established initially around a Scientific Advisory Board consisting of nine members, including Kenneth Murray, who recommended projects to be pursued by the company, some of which were initiated in the University laboratories of the Board members. One such project was the Hepatitis B project pursued by Kenneth Murray at the University of Edinburgh, which was one of the company's early scientific successes. This success hinged on the licensing arrangements under its patents relating to Hepatitis B antigens for both diagnostic and vaccine purposes. An agreement put in place with the University of Edinburgh ensured that the University would receive a proportion of the patent royalties as well as a royalty on sales of products manufactured and sold by the company. Biogen also had a Supervisory Board of Directors comprising representatives of the venture capitalist sponsors of the company, the financial community and members of the Scientific Board.

Biogen opened its own research laboratories in Geneva in 1979. As the company's financial strength grew, additional laboratories were established in Cambridge, Massachusetts. This enabled Biogen to benefit from the intense scientific activity in the area of genetic engineering and related technologies in the United States, and the proximity of some of the Scientific Board members at Harvard and MIT. In 1983 Biogen became a public company with its stock trading on Wall Street. The company sold its Geneva operations to Glaxo in 1987.

Biogen originally derived income from licensing arrangements of its technology, patents and products with various pharmaceutical companies, but by the end of 1983 it was decided to concentrate on high value products in the pharmaceutical industry, an approach which proved too resource-heavy for the company. After a period of retrenchment, Biogen's fortunes began to revive under a new Chief Executive Officer, James Vincent, who joined the company in 1985. A company restructure, new licensing arrangements and a focus on select scientific areas and products which the company could develop itself, saw Biogen operating close to a 'break even' situation by 1988.

In 2003, Biogen merged with San Diego, California-based IDEC Pharmaceuticals and adopted the name Biogen Idec. After the merge, Biogen Idec became the third largest biotechnology company in the world. Following shifts in research core areas, the company reverted to the shorter name of Biogen. In the following years it went on to acquire several other pharmaceutical companies, including Conforma Therapeutics and Syntonix Pharmaceuticals.