Lipinski received his PhD from the University of California, Berkeley in 1968 in physical organic chemistry. The Advanced Drug Delivery Reviews article reporting his "rule of five" is one of the most cited publications in the journals history. In 2006, he received an honorary law degree from the University of Dundee and he has won various awards, including being the Society for Biomolecular Sciences winner of the 2006 SBS Achievement Award for Innovation in HTS.