In 1996, he began working for Cytel Corporation, where he was vice president, chief scientific officer, and member of the Board of Directors.
In 2001, he became principal researcher and founding director of the National Institutes of Health-funded Consortium for Functional Glycomics.
[3][4] Paulson is currently Cecil H. and Ida Green Professor and co-chair of Department of Molecular Medicine[5] at The Scripps Research Institute.
[15] Paulson is currently a Glycobiology (journal) editor[16] and past-chair of the American Chemical Society Division of Carbohydrate Chemistry.
[17] He is also an advisory board member for: the Joint Center for Structural Genomics, PSI Biology; the Boston University Mass Spectrometry Resource; Alberta Glycomics Centre;[18] Institute for Biological Sciences, NRC, Ottawa; Center of Excellence in Influenza Research and Surveillance, St. Jude Children's Research Hospital and Glyco-Net.