Born on December 4, 1986, in Houston, Texas, he was a two-sport star at Memorial High School, splitting time between football and baseball, before he suffered a back injury ending his brief football career.
He hit .413 as a junior, with 4 home runs and 23 RBIs in 2004. He had a .519 batting average and was named all-state in his senior year. As a pitcher, he had a 7–1 record and a 1.75 ERA.
He signed with the University of Texas at Austin (where his father played) to play first base on November 17, 2004, but never attended, choosing to go straight to professional baseball after he was drafted by the Houston Astros.
The Houston Astros picked Clemens in the 8th round of the amateur draft, 254th overall. The Astros organization has intended to use him as either a first or third baseman. He signed for a $380,000 bonus.
In 2005, he played his first minor league baseball season, hitting .297 with 4 homers and 17 RBIs in 33 games for the Rookie League Greeneville Astros, and .281 with 6 RBIs in 9 games with the Class A Tri-City ValleyCats. He committed 15 errors in 32 games at third base.
In 2006, he played for the Single-A Lexington Legends of the South Atlantic League, where he batted .229 with 5 home runs and 39 RBIs in 91 games. Clemens' sole appearance as a pitcher in professional baseball was for the Legends in 2006.
On June 25, 2006, Clemens was in the news in a game against the Asheville Tourists. He was declared safe in a controversial play on second, leading Tourists manager Joe Mikulik to go on a rampage. Through 2006, in the minors he has batted .249 with 9 home runs, 63 RBIs, 7 stolen bases (while being caught once), and a .385 slugging percentage in 449 at bats.
In the 2006 Hawaiian Winter League, playing for North Shore Honu, Clemens batted .196 with 1 home run and 9 RBIs in 32 games.
Koby Clemens hit a home run off of his father, Roger Clemens, in a 2006 minor league exhibition game. In Koby's next at bat, Roger threw a brushback pitch at Koby in retaliation.
He converted to play as a catcher and had played for the Corpus Christi Hooks in the Double-A Texas League. As of June 12, 2009, he returned to play for the Lancaster JetHawks in Advanced A in the California League in the roles of catcher and designated hitter.
In 2011, Koby was with the Houston Astros' Triple-A affiliate, the Oklahoma City RedHawks of the Pacific Coast League, as their first baseman.
Clemens started playing at the Puerto Rico Baseball League with the Mayagüez Indians as a first baseman in the fall of 2011. However, he abandoned the team abruptly on November 10, 2011. There were rumors that his father, former MLB pitcher Roger Clemens, persuaded him to leave the island because of the kidnapping of Washington Nationals catcher, Wilson Ramos in Venezuela the day before. For abandoning the team with no reason given, Koby has been banned from playing baseball in the Caribbean Baseball Confederation.
On February 9, 2012, Clemens signed a minor league contract with the Toronto Blue Jays. During the 2012 season, he played for the Blue Jays' Double-A affiliate, the New Hampshire Fisher Cats of the Eastern League, and their high Single-A team, the Dunedin Blue Jays of the Florida State League as a catcher, first baseman, third baseman, oufielder, and designated hitter. He was released at the end of the season.
Koby played in the California Winter League in Palm Springs, California from January 18 to February 16, 2013. As of May 2014 he was on the active roster of the Sugar Land Skeeters.
On February 13, 2015, it was announced that Clemens will be a minor league spring instructor for the Astros farm system. Astros Director of Player Development Quentin McCracken said that the Astros "expect by the end of the year or by next season he will be on staff fully." He now owns his own baseball company called Koby Clemens Baseball Clinics and teaches individual and private lessons.