He was 72.
Susan Spilka, a spokeswoman for the family-owned publishing company, said Ellis died of cancer, The New York Times reported Sunday.
Ellis was president and chief executive from 1990 to 1998, taking over after the company made unsuccessful ventures into business education and training.
"There was a period in the '80s when the company floundered, and he brought it back to profitability," Spilka said.
Under Ellis' watch, the company was listed on the New York Stock Exchange and began putting all of its journals online in 1997. He also made Wiley one of the first publishers to develop a digital object identifier -- or DOI -- system, for embedding identifying marks in electronic books and journals to track their use on the Internet, the newspaper said.
Charles Richard Ellis was born in Manhattan July 20, 1935. He graduated from Princeton and later received a master's degree from Columbia.
He is survived by his wife Sandi, a son, four stepchildren, nine grandchildren and one great-grandchild.