He appeared for the Jamaican U-20’s in the 2001 FIFA World Youth Championship in Argentina and made his debut for the ‘Reggae Boyz’ in 2004 against Guatemala. He has earned 32 caps (3 goals).

Upon graduating, Stephenson was drafted 27th overall in the 2004 MLS SuperDraft by Chicago Fire. He did not make the Fire team, however, and was traded to Kansas City Wizards for a third-round 2005 MLS SuperDraft pick. Stephenson played very little for the Wizards in his rookie season, finishing the year with no points, having played only 44 minutes over three games. He became a starter in the playoffs, playing in every game and even scoring a goal on the Wizards’ run to the final.

In 2006, Stephenson made his move to Scandinavia, starting in Sweden with GAIS, where he had an outstanding season as a midfielder. He then made a move to AIK in 2007, where he had an inconsistent season for a team that finished in the top half of the league. In August 2008, Khari then moved to Aalesunds FK in Norway, where he was joined by Jamaican international teammate Demar Phillips in the midfield. After not receiving significant playing time in early 2009, he gained a vital midfield role as the season progressed, eventually leading the team to the Norwegian Cup in 2009 and qualification for the 2010/11 Europa Cup.

Stephenson returned to the United States on loan from Aalesunds FK and signed with the San Jose Earthquakes of Major League Soccer on 9 August 2010 until the remainder of the MLS season. Stephenson returned to Norway and then signed a permanent deal on 14 February 2011 with San Jose Earthquakes.

On 22 February 2013, he was signed by Real Salt Lake. He played one season in Utah; however, he was not retained following the season.

Stephenson signed for his old club San Jose Earthquakes on 11 March 2014. Stephenson scored 2 goals during the 2014 season.

On 6 August 2015, Stephenson was loaned from San Jose to San Antonio Scorpions of the North American Soccer League.