Bouknight was born in Columbia, South Carolina and graduated from Brookland-Cayce High School in 1997. He was selected as an All-Star by the South Carolina Baseball Coaches Association in his senior year. During a playoff match-up against Union High School that year, he threw a no-hitter. In 1995, his sophomore year, he was named as an honorable mention from South Carolina in the All-USA High School award.
Bouknight was a four-year starting pitcher at the University of South Carolina and set career records at the university in innings pitched (482.0), strikeouts (457), games won (45) and games started (57). He finished with a 45-12 career record. With his 45 wins, Bouknight is tied with Jeff Brantley for the all-time SEC record.
Bouknight finished the 1998 season with a record of 6-1 and a 2.21 ERA. In that season, he earned first-team All-SEC, SEC All-Freshman Team and Freshman All-American honors. In honor of his break-out season, the University baseball team awards the Kip Bouknight Award to the best freshman pitcher each season.
As a junior in 2000, he earned the most wins of any collegiate pitcher with 17 that year, only lost one game, and posted a 2.81 ERA. He was named a consensus All American. He was named to the first-team All-SEC team, SEC Pitcher of the Year and SEC Male Athlete of the Year.
Bouknight also won several national Player of the Year honors in 2000 including the Golden Spikes Award as the nation's top amateur player and the Rotary Smith Award as the most outstanding collegiate pitcher.
In 2007, he was inducted into the University of South Carolina Athletic Hall of Fame.