While playing for the University of Georgia (UGA), Lilliquist was selected as Baseball America's Pitcher of the Year and was an All-American in 1987.

[3] He helped lead to UGA to their first-ever Southeastern Conference title and trip to the College World Series.

He was promoted to the Durham Bulls of the Carolina League, where he made three starts, totaling 25 IP, two complete games and a 2.88 ERA.

On May 1, 1990, at Atlanta in Atlanta–Fulton County Stadium, Lilliquist became one of the few pitchers to have a multi-homer game when he hit two home runs off Ron Darling in a Braves' 5–2 victory over the New York Mets.

With a 6.28 ERA and two wins and eight losses in 11 starts, the Braves traded Lilliquist to the San Diego Padres for Mark Grant on July 12, 1990.

Lilliquist's only career MLB complete game and shutout occurred on August 12, 1990, in a 9–0 defeat of the Houston Astros.

He signed as a free agent with the Boston Red Sox before the 1995 season, but could not replicate his success in Cleveland.

The Los Angeles Dodgers signed Lilliquist on August 1, 1995, and assigned him to their AAA minor league affiliate, the Albuquerque Dukes.

The Reds assigned him to their AAA minor league affiliate, the Indianapolis Indians, where he appeared in 47 games – all as a reliever – and posted a 2.60 ERA.

Palm Beach won the 2005 FSL Championship as the pitching staff registered the league's second-best ERA at 3.94.

[1] He then contributed as the Cardinals' pitching coordinator from 2008–10, helping to rehabilitate injured pitchers at the club's spring training complex in Jupiter.

[11] Late in the Cardinals' 2011 World Series–championship season, he temporarily replaced incumbent pitching coach Dave Duncan, who took a leave of absence for family reasons.

On January 6, 2012, the Cardinals announced that Lilliquist would permanently replace Duncan, whose future remained uncertain.