The Trojans announced Wednesday that longtime assistant Mark Smartt will take over the program.
Pierce is a two-time Sun Belt Conference coach of the year. He has led the Trojans to four conference titles and four NCAA regionals since taking over in 2003.
Troy won a share of the Sun Belt title last season and lost to Florida State in the regional finals.
Smartt has been on Pierce's staff during his entire tenure. A former second baseman, he helped lead the Trojans to Division II national championships in 1986 and '87 and finished with the third-highest career batting average in school history.
"No one is more qualified to take over this program than Mark Smartt," Troy chancellor Jack Hawkins said.