In June 2007, Azar was hired by Eli Lilly and Company chief executive officer Sidney Taurel to be the company's top lobbyist and spokesman as its Senior Vice President of Corporate Affairs and Communications.[6][19] Azar left the position after the 2008 United States presidential election was won by Democratic Party candidate Barack Obama and the corporation wanted to replace Azar with a Democrat in that role.[citation needed]

In April 2009, Azar became Vice President of Lilly's U.S. Managed Healthcare Services organization and its Puerto Rico affiliate.[20] In 2009, the company paid $1.415 billion to settle criminal charges regarding its promotion of antipsychotic drug Zyprexa (olanzapine) for off-label uses between 1999 and 2005.[19]

Effective January 1, 2012, Azar became President of Lilly USA, LLC, the largest division of Eli Lilly and Company, and was responsible for the company's entire operations in the United States.[20] Prices for drugs rose substantially under Azar's leadership, including the tripling of the cost of the company's top-selling insulin drug. Also under Azar's watch, Eli Lilly was one of three companies accused in a class-action lawsuit of exploiting the drug pricing system to increase profits for insulin. Eli Lilly was also fined in Mexico for colluding on the price of insulin.[21][22] In connection with the position, Azar served on the board of directors of the Biotechnology Innovation Organization, a pharmaceutical lobby.[23]

In January 2017, Azar resigned from Eli Lilly "to pursue other career opportunities" as a result of a company reorganization.[24] He also resigned from the board of directors of the Biotechnology Innovation Organization. In his last year at the corporation he earned $2 million.[25]