A native of Joliet, Illinois, Michalak attended Joliet Catholic Academy and the University of Notre Dame. In 1991, he played collegiate summer baseball with the Chatham A's of the Cape Cod Baseball League.
Michalak was selected by the Oakland Athletics in the 12th round of the 1993 MLB Draft. He signed as a free agent with the Arizona Diamondbacks in 1997, and made his major league debut with Arizona in 1998. His most productive season came in 2001, when he tossed 136.2 innings while splitting time for the Toronto Blue Jays and Texas Rangers. His final major league appearance came in 2006 for the Cincinnati Reds.
Michalak played for the Washington Nationals Triple-A affiliate, the Columbus Clippers, in 2007. On June 14, 2008, Michalak signed a minor league contract with the Florida Marlins and was assigned to their Triple-A affiliate, the Albuquerque Isotopes. After his release from the Marlins organization, he signed with the Oakland Athletics and assigned to their Double-A affiliate, the Midland RockHounds, on August 2, 2008. He became a free agent at the end of the season. On April 26, 2009, Michalak signed a minor league deal with the Toronto Blue Jays.

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