He started his career for Sparta where he stood out for his technical skill and subsequently signed for Ajax where he made his debut against FC Groningen on 1 September 2002. In 2006, he joined French league side Nantes but in January 2007 he was loaned to AZ. Although not unsuccessful, AZ chose not to buy him and Boukhari returned to Nantes, who were relegated. Boukhari was reluctant to play in the second division and on 7 July he returned to Sparta, where he signed a contract for three years. Back at the club where it all started for him, Boukhari became club captain and the face of the 100-year Anniversary of the club.
After spending a season with Sparta Rotterdam, Boukhari was approached early in the transfer window by Saudi Arabian club Al-Ittihad. However, the Saudi Arabian side then refused to pay the transfer fee to Sparta, instead of paying the fee, sending a lawyer to declare that they wanted to cancel the deal. Al-Ittihad manager Gabriel Calderón was reportedly unhappy about Boukhari's lack of match fitness, and asked the board to cancel the transfer. However, the Eredivisie side wanted the transfer to go through: “The transfer is a done deal and we expect to receive the money into our account,” said director Peter Bonthuis. The Rotterdam side submitted a complaint to FIFA regarding the Saudi Arabian club's sudden change of action.
In January 2009 Boukhari signed a contract till the end of the season with NAC Breda, and in July 2009 he signed three-year deal with Kasimpasa SK in Turkey.