Champak received his undergraduate degree in Chemistry (First Class) from the University of Bombay, and an MS in Organic Chemistry from I.I.T. Bombay (Institute Silver Medal), where he worked with Dr. Sambasivarao Kotha. He performed doctoral studies in the research group of Dr. Wilfred A. van der Donk at the University of Illinois at Urbana-Champaign, where he studied the mechanism of lantibiotic biosynthesis and developed a keen interest in the biology of post-translational protein modification. His post-doctoral work in Dr. Tom W. Muir‘s laboratory of Synthetic Protein Chemistry at Rockefeller University focused on understanding the mechanism by which ubiquitin stimulates histone methylation, and developing new methods for the site-specific modification of proteins with ubiquitin and ubiquitin-like proteins.