Petroskey was elected to the Presidency of the National Baseball Hall of Fame and Museum on June 15, 1999. During his tenure as the President of the Hall, Petroskey was credited with expanding membership and fundraising, furthering educational efforts and outreach, and establishing a closer relationship with the business of baseball with which the Hall had not always been on the best of terms. Under his leadership, the Hall embarked on a major renovation and modernization, which was completed in 2005 at a cost of $20 million. He has also been credited for the Hall's early 2000s initiatives to increase and further recognition of the contributions of Negro League players, managers, and executives, continuing an effort first broached by Hall of Famer—and Negro Leaguer-- Jackie Robinson. A five-year program resulted in the elevation of 17 Negro Leaguers to members of the Hall of Fame in 2006. He was president during the 2007 induction ceremony, which saw a record-breaking crowd of over 82,000 people in Cooperstown, as well as the 1999 ceremony which saw 50,000 people, tied for second-most ever.
"Bull Durham" censorship controversy
In April 2003, one month after the start of the Iraq War, Petroskey caused a furor when he canceled an event meant to commemorate the 15th anniversary of the well-known 1988 baseball movie Bull Durham because of the anti-war stance of two of its stars, Tim Robbins and Susan Sarandon, fearing that they would use the event as a platform for their political views. Petroskey, a former assistant press secretary in the Reagan administration, sent Robbins and Sarandon a letter that said: "We believe your very public criticism of President Bush at this important - and sensitive - time in our nation's history helps undermine the U.S. position, which ultimately could put our troops in even more danger." Robbins responded: "Long live democracy, free speech and the '69 Mets - all improbable, glorious miracles that I have always believed in." Many people, including well-known baseball figures like authors Roger Kahn and Jules Tygiel, were upset by what they saw as an attempt to punish political speech. Kahn canceled an appearance at the Hall and Tygiel called for Petroskey's resignation. Bull Durham co-star Kevin Costner defended Robbins and Sarandon, saying, "I think Tim and Susan's courage is the type of courage that makes our democracy work... Pulling back this invite is against the whole principle about what we fight for and profess to be about."
His resignation was tendered under pressure on March 25, 2008 for "fail to exercise proper fiduciary responsibility" while making "judgments that were not in the best interest of the NationalBaseball Hall of Fame and Museum." Petroskey was replaced by one of his vice-presidents, Jeff Idelson.