General manager Josh Byrnes confirmed on Friday that Madison, who was hired in December 2009, will be reunited in Chicago with Padres' former assistant GM Jason McLeod and, of course, former San Diego GM Jed Hoyer.
Madison, who got his start in scouting with the organization in 2002, had three stints with the Padres and worked closely with McLeod on two of them.
McLeod and Madison worked together on the Padres' Drafts in 2010 and 2011. This past June, Madison worked with Chad MacDonald, assistant GM of player personnel, the main overseer of the Draft in his first full season with the organization.
"Jaron did a great job for us. ... I wish him nothing but the best with the Cubs," Byrnes said. "We have got a great staff here. Jaron was a big part of that."
Byrnes hopes to name a replacement in the next two weeks or so.
McLeod and Madison had what many regarded as a superlative Draft in 2011, when the team selected second baseman Cory Spangenberg in the first round and later added pitchers Joe Ross, Matthew Wisler, Matthew Andriese, Kevin Quackenbush, Burch Smith and Matthew Stites, in addition to second-round catcher Austin Hedges and shortstop Jace Peterson, a compensation-round selection.
After this year's Draft, MacDonald and Madison, working with tougher and more prescribed bonuses thanks to the Collective Bargaining Agreement, signed their first 17 overall picks and 23 of their first 24 selections.
Madison is a 1998 graduate of Long Beach State University, where he played baseball for coach Dave Snow. He joined the organization in 2002 before leaving to become an area scout for the Pirates, and returned to San Diego in 2005 to serve as an assistant to the director of scouting. He then spent two years as assistant director of scouting for the Cardinals before once again returning to San Diego.