Mercker was born in Dublin, Ohio. He was taken in the first round (5th pick overall) of the 1986 Major League Baseball Draft by the Atlanta Braves. He made his major league debut with the Braves on September 22, 1989, and appeared in two games that season.

Mercker has taken part in two no-hit games during his career, both with the Braves. The first, on September 11, 1991, against the San Diego Padres at Fulton County Stadium, was a combined effort between Mercker, the starter, who pitched six innings; Mark Wohlers, who pitched the seventh and eighth innings; and Alejandro Peña, who pitched the ninth. The Braves defeated the Padres 1-0. The second no-hitter was a solo effort by Mercker, as he no-hit the Los Angeles Dodgers on April 8, 1994, at Dodger Stadium in a 6-0 victory. To date, this no-hitter is the last to be pitched by a Brave.

After the 1995 season, the Braves traded Mercker to the Baltimore Orioles. Mercker then became a journeyman, spending time with Baltimore (1996), Cleveland (1996), Cincinnati (1997, 2003, 2005-2006, 2008), St. Louis (1998-1999), Boston (1999), Anaheim (2000), Colorado (2002), Atlanta (2003), and the Chicago Cubs (2004). He signed with Cincinnati for the third time in his career on December 20, 2004.

Mercker received the Tony Conigliaro Award in 2000 following his recovery from a cerebral hemorrhage.

On February 8, 2008, Mercker signed a minor league contract with Cincinnati with an invitation to spring training. He pitched in 15 games for the Reds that season. He currently works as a broadcaster for the Reds.