Diop was born in Rufisque, Dakar. He began his football career with junior team Ndeffann Saltigue before joining ASC Diaraf of the Senegal Premier League in 1996. He left Senegal for Switzerland, where he spent a few months with third-tier club Vevey before signing as a professional for Ligue Nationale A club Neuchâtel Xamax in the 2000 close season. In December that same year, he joined fellow top-flight club Grasshoppers, whom he helped to the championship title in his first half-season and made his first appearance in UEFA competitions the next. He moved to France in January 2002 to join Lens of Ligue 1 on a five-and-a-half-year contract.

Bouba Diop got his first call up to the Senegal national squad in 1999, at the age of 21, while playing for Neuchâtel Xamax in the Swiss Super League. He is perhaps best known for scoring the first goal of 2002 FIFA World Cup against France, which resulted in the 1–0 defeat of the then reigning World champions and ultimately, their early elimination from the tournament, in which Senegal reached the quarter-finals. He ended as his team’s best scorer of the tournament with three goals, having also scored twice against Uruguay. Diop has played 63 times for Senegal scoring 11 goals.

After his impressive performances for Lens, Papa Boupa Diop signed with Premier League team Fulham for £6 million, signing a four-year deal in July 2004. Diop made his debut against Manchester City on 14 August 2004, playing the full 90 minutes. Diop scored his first goal for Fulham against Chelsea, scoring Fulham’s only goal in a 4–1 home defeat. In his first season at Fulham, Diop made such an impressive display for the club that he was named Fulham’s Opta player of the season award for 2004/05.

For his performances during the 2005–06 season, Diop was nominated for the Fulham “Player of the Year” award. Diop would then signed a new deal that will keep him until 2009. Diop then said that he made a right decision to sign a contract with Fulham. Diop became a fans’ favourite. In 2005, he was appointed as captain by Coleman.

An injury due to hamstring, foot, and back problems resulted in him missing part of the 2006–07 season and losing the captaincy to Danny Murphy. In January 2007 Wigan Athletic made a £5 million bid for the midfielder, but Diop decided against the move and stayed with Fulham, helping them to avoid relegation.

Diop signed a five-year deal with Portsmouth for a fee of £3.5 million. He made his debut against Liverpool on 15 September 2007 in a 0–0 draw. Diop was a key player in Portsmouth’s victorious 2008 FA Cup campaign, playing a solid, defensive game and making some crucial tackles against Cardiff City.

Following Portsmouth’s relegation, Diop was considered likely to be released. Portsmouth’s administrator, Andrew Andronikou, stated that Diop would only be leaving for a fee of £1 million, but Portsmouth eventually agreed to a €300,000 offer from AEK Athens in July 2010. He played 72 games for Portsmouth without scoring.

On 13 July 2010, Diop agreed terms with AEK Athens signing a two-year deal earning €900,000 per season, despite interest from Fulham, Celtic and Paris Saint-Germain.

Diop made his debut for AEK Athens against Dundee United on 19 August 2010. He did not play the full 90 minutes as he was not fully fit recovering from his injuries. Diop scored his first Super League goal against PAOK, the match finished 4–0 to AEK. Bouba Diop finished the season only playing 19 games due to constant injuries. On 30 April 2011, Diop won the Greek Cup with AEK in a 0–3 win against Atromitos and was a key player in the victory playing a very solid game. Diop also scored two goals against PAOK in the Superleague Greece play-off’s giving AEK the 3–0 lead. Diop was also awarded the MVP award.

On 30 August 2011, West Ham announced the signing of Diop on a one-year deal. He joined on a free transfer after leaving AEK Athens. The deal included an option to sign for a further year. He made his debut for West Ham on 1 October 2011 in a 2–2 away draw with Crystal Palace. He scored his first and only goal for West Ham, against Barnsley on 17 December 2011. His goal proved to be the winner in a 1–0 win. On 30 June 2012, Diop was released by West Ham on expiry of his contract.

In October 2012, he agreed terms to join former teammate Lee Clark’s Birmingham City on a short-term contract, subject to successful application for a working visa, and the deal was completed on 19 October. He then signed for a further month, and finally made his Birmingham debut as a second-half substitute in a 1–1 draw away to Blackpool on 27 November. He was booked within minutes of entering the game. With Hayden Mullins suspended and Jonathan Spector injured for the visit of Crystal Palace on 15 December, Diop made his first start for Birmingham, alongside League debutant Callum Reilly in central midfield. He scored the equalising goal, a powerful header from Rob Hall’s corner, as Birmingham came back from 2–0 down to draw, and was rewarded with another month’s contract. He injured a hamstring soon afterwards, and despite his imminent return to fitness, the club’s financial difficulties meant they could not offer him a further contract extension. He left the club in January 2013.