In 2002 Pestell was named director of the Lombardi Cancer Center, the Francis L. and Charlotte Gragnani Endowed Chair, and chairman of the Department of Oncology at the Georgetown University Medical Center. During this tenure, he also served as associate vice president of the Georgetown University Medical Center, at the Georgetown University School of Medicine. While serving as director of the Lombardi Cancer Center, Pestell led the effort for renewal of its National Cancer Institute designation, and founded the Capital Breast Care Center with Andrea Jung of the Avon Foundation. In 2003 he was also named president of the US branch of the International Network for Cancer Treatment and Research.