After leaving the Massachusetts Institute of Technology, Pedersen became employed at the DuPont Company in Wilmington, Delaware in 1927 through connections from his research advisor, Professor James F. Norris. While at DuPont, Pedersen was able to begin research at the Jackson Laboratory under William S. Calcott and finished his career with DuPont at the Experimental Station in Wilmington, Delaware.As a young chemist at DuPont, Pedersen witnessed and gained inspiration many flourishing chemists such as Julian Hill and Roy J. Plunkett, and also breakthroughs in polymers and work in the field of organic chemistry.[10] Pedersen had a particular interest in industry as he started his focus on his chemical career, which influenced the direction of problems he set out to solve as a chemist. As Pedersen began working on problems as a new chemist, he was free to work on whatever problems fascinated him and he quickly became interested in oxidative degradation and stabilization of substrate. Pedersen's papers and work expanded beyond this, however it was a major influence to his eventual Nobel Prize awarded research.
Retiring at the age of 65, his work resulted in 25 papers and 65 patents, and in 1967, he published two works describing the methods of synthesizing crown ethers (cyclic polyethers). The donut-shaped molecules were the first in a series of extraordinary compounds that form stable structures with alkali metal ions. In 1987, he shared the Nobel Prize in Chemistry for his work in this area with Donald Cram and Jean-Marie Lehn, whom expanded upon his original discoveries.