Hinch was released by the Royals after the 2002 season. He signed as a minor league free agent with the Cleveland Indians, but was purchased by the Detroit Tigers from the Indians in March 2003. He signed with the Philadelphia Phillies for the 2004 season, splitting the year between the majors and Triple-A. He spent all of 2005 with the Phillies' Triple-A affiliate before retiring.
After the 2005 season, Hinch was hired by the Arizona Diamondbacks as their manager of minor league operations. Even while playing, he was planning his post-playing career. He went so far as to go to the 2003 General Manager's winter meetings to look for future job opportunities and contacts. In July 2006, Baseball America named him one of baseball's "10 to watch" in the next 10 years for his promise as a Farm Director and future General Manager. In August 2006, the Diamondbacks named Hinch director of player development.
Hinch was named manager of the Arizona Diamondbacks on May 8, 2009, replacing Bob Melvin, even though he had never managed or coached a team at any level. Hinch, at age 34 years and 357 days, became the youngest person to be named manager of a Major League team since Eric Wedge (34 years, 275 days).
Hinch was fired from the Diamondbacks on July 1, 2010, following a 31–48 start to the 2010 season. Overall, Hinch compiled an 89–123 record in 212 games. His .420 winning percentage ranks as the second lowest in Diamondbacks history, just ahead of Al Pedrique.