Born in Linyola, Lleida, Catalonia, to a Serbian father, Bojan Krkić Sr., who was a professional footballer for Serbian side OFK Beograd, and a Catalan mother, Maria Lluïsa Pérez, Bojan played for Barcelona's youth teams from 1999 to 2006. A quick striker with quite notable dribbling skills, it was reported that he scored over 900 goals for various youth teams since joining the club as an eight-year-old, breaking Lionel Messi's record. He then played the 2006–07 season with the Barcelona B team until he signed a professional contract with the first team upon turning 17. Bojan played his first match with Barcelona on 24 April 2007, scoring a goal in a friendly match against Egyptian club Al Ahly.
On 16 September 2007 (at 17 years and 19 days), Bojan made his official debut for Barcelona against Osasuna, replacing Giovani dos Santos in the 78th minute and breaking Lionel Messi's record of the youngest Barcelona player to feature in a La Liga match. Three days later, he made his UEFA Champions League debut against Lyon, coming on at the 88th minute for Messi. He was, at the time, the youngest Barcelona player ever to feature in a Champions League game, at 17 years and 22 days. He made his second Champions League appearance on 2 October, coming on at the 81st minute for Ronaldinho against VfB Stuttgart. On 20 October 2007 (at 17 years and 53 days), Bojan made his first league start for Barcelona away to Villarreal and scored in the 25th minute. It was his first goal for the club's first team and it made him the youngest ever goalscorer for Barcelona in a league match.

Bojan scored his first ever Champions League goal on 1 April 2008 (at 17 years and 217 days) against Schalke 04, netting the only goal in the first (away) leg of the quarter-finals, making him the first person born in the 1990s to score in the Champions League, and the youngest player to score in the knockout phase. Bojan finished the season with a record of ten goals, breaking Raúl's record of most goals scored in a debut season.
Upon the departure of Gianluca Zambrotta, Bojan was handed the number 11 shirt. After 14 games (13 of which he entered as a substitute), Bojan ended a goal drought by netting a brace against Almería in a 2–0 victory. Despite featuring less compared to the previous season, Bojan helped Barcelona to their 19th La Liga title. He also aided Barcelona to their first Copa del Rey win in 11 years by scoring five goals in the competition, including one in the final against Athletic Bilbao. Bojan was an unused substitute in the 2009 UEFA Champions League Final against Manchester United, which Barcelona won 2–0 and saw them cap off a treble-winning campaign. Bojan's three goals in ten appearances throughout the competition saw him finish as the equal sixth-highest goalscorer for the season.
On the first day of the 2009–10 La Liga campaign against Atlético Madrid, Bojan scored a header in the 18th minute courtesy of …

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Bojan shot to prominence as a 15-year-old at the UEFA European Under-17 Championship in Luxembourg in May 2006 when he was joint top-scorer, despite being a year younger than most of the other players in the tournament and only playing 40 minutes in four out of Spain's five matches. He scored a hat-trick against Luxembourg before inspiring his side to a 3–0 victory over the eventual champions Russia, with all of the goals being scored after he came on as a second-half substitute. In the third match, he scored a penalty after once again being introduced at half time. He started the semi-final against the Czech Republic but, after his teammate Roberto García was sent off, Spain struggled and lost 0–2 in a shock result. In the third-place play-off, Bojan was once again a second-half substitute and scored the opener in the 53rd minute. When the match went to penalties, he scored and Spain won 5–4 to finish third. In the 2007 European Under-17 Football Championship, Bojan led Spain to victory, scoring the only goal against England in the final. He also scored in the semi-final against Belgium.

There was controversy surrounding Bojan's call up to the Spain U17 squad for the 2007 FIFA U-17 World Cup in South Korea, because Barcelona wanted to keep him so that he could be part of their Asian tour. The Royal Spanish Football Federation (RFEF) denied the request, and further controversy arose when the RFEF denied one of Barcelona's medics, Ricard Pruna, the opportunity to accompany Bojan to the tournament to monitor a tendon problem in the player's knee.

During the tournament, Bojan scored five goals, finishing as joint third top scorer along with Germany midfielder Toni Kroos. He was inspirational in leading Spain to the final. In the semi-final against Ghana, however, Bojan was sent off for his second yellow card with only seconds left to play. He was suspended for the final and Spain lost to Nigeria on penalties. Because of his performances, Bojan was given the Adidas Bronze Ball, naming him the third best player in the tournament, behind Nigeria's Macauley Chrisantus (silver) and Toni Kroos (gold).

Bojan scored for the Spanish under-21s in their 2–0 win over Poland, on 12 October 2007, quickly establishing himself as an important player, also prompting rumours of an eventual call-up from senior side's manager Luis Aragonés. Bojan was selected in the squad for the 2009 UEFA Under-21 Championship. The Spanish team, however, underperformed and picked up one point from their first two games, leaving progression almost impossible. Bojan was called up to the Spain U-21 squad for 2011 UEFA European Under-21 Football Championship.
Bojan was approached to play for Serbia in 2008 but declined because of his wish to play for Spain. He was included in the …

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On 13 September 2023, he became the football coordinator at his former club Barcelona, with his main task being monitoring the youngsters at La Masia, along with head of youth department, Alexanko.