Kljestan played for the Region IV Olympic Development Program team. He then played three years college soccer at Seton Hall University. He was named first team All-American in 2004 and earned third team honors in 2005. Kljestan was named Big East Offensive Player of the Year in 2005 and earned first-team All-Big East in 2004 and 2005. He holds the single-season assists record at Seton Hall with 15 in 2005 and ranks fifth all-time at the school with 28 over a three-year career. Kljestan finished his college career with 20 goals and helped Seton Hall University to three NCAA Tournament appearances. He then signed a Generation adidas contract with MLS, and played USL Premier Development League soccer for Orange County Blue Star in 2005. Kljestan was taken fifth overall at the 2006 MLS SuperDraft.
Kljestan was part of the United States Under-20 team at the 2005 World Youth Championship. In early 2007, Kljestan was called into training camp with the senior United States men's national soccer team, but did not earn a cap in the following games. Kljestan made his debut for the senior United States men's national soccer team on June 2, 2007 with an assist in a 4-1 friendly match victory over China in San Jose, California.
He was a finalist for 2006 MLS Rookie of the Year and played for the US in Copa América 2007. He also played for the US Under-23s at the 2008 CONCACAF Men's Pre-Olympic Tournament and scored in a 3-0 win against Canada to send the US Under-23s through to the Olympics.
He was nominated for the Starting XI in the 2008 MLS All-Star Game, but chose instead to play for the U.S. Olympic Team in the 2008 Beijing Olympics.
His brother Gordon currently plays for the New York Red Bulls of MLS. Kljestan's father, an ethnic Serb, was a semiprofessional player in Yugoslavia.