The shop bested Bcom3 Group's Starcom Worldwide and WPP Group's Mediaedge:CIA.
Eli Lilly suffered a major hit last year when its flagship anti-depressant drug Prozac began to face generic competition.
The company also co-markets diabetes drug Actos and its osteoperosis drug Evista competes with Merck's Fosamax. Evista featured actress Julie Andrews in some creative.
Staff writer David Goetzl contributed to this report.