He worked as part of the DNA synthesis group at Genentech from 1986 to 1990, before joining Gilead in 1990 as Director of Organic Chemistry. In 1993, he began work, as head of a team, to create Tamiflu. In 1996, clinical studies were carried out on the drug, which was the first orally active commercially developed anti-influenza medication. Explaining the motivation behind this, he said, "We decided to create a pill and not a medication to inhale because especially people who suffer from influenza struggle with breathing difficulties. And the agent would only reach the lung," Three years later, the right to market and develop Tamiflu were sold to Roche, with Bischofberger and Gilead retaining the intellectual rights to it.
Bischofberger has publicly displayed pessimism over the risk viruses pose, saying, "I think the threat by new bacterial or viral agents is higher than the potential of a nuclear war."