Sharpless was born April 28, 1941, in Philadelphia, Pennsylvania. His childhood was filled with summers at his family cottage on the Manasquan River in New Jersey. This is where Sharpless developed a love for fishing that he would continue throughout his life, spending summers in college working on fishing boats. He graduated from Friends Central School in 1959, and continued his studies at Dartmouth College, earning an A.B. in 1963. Sharpless originally planned to attend medical school after his undergraduate degree, but his research professor convinced him to continue his education in chemistry. He earned his Ph.D. in Organic Chemistry from Stanford University in 1968 under Eugene van Tamelen.  He continued post-doctoral work at Stanford University (1968–1969) with James P. Collman, working on organometallic chemistry. Sharpless then moved to Harvard University (1969–1970), studying enzymology in Konrad E. Blochs lab.