His father, also namedBojan Krkic, is a Serb and a former footballer, who played for Red Star Belgrade and for FK Sutjeska in the 1980s. After moving to Spain his father married Maria Lluïsa Pérez, a Spanish nurse, and became a scout for Barcelona in 1997.

Bojan Krkic played for FC Barcelona's cantera from 1999 to 2005, scoring more than 800 goals in seven years, breaking all previous goal scoring records held at the club's youth levels. A quick striker, with quite notable dribbling skills, Bojan played the 2006–07 season with the FC Barcelona B team until he signed a professional contract with the Barcelona A team upon turning 17. Bojan played his first match with Barcelona on April 24, 2007, scoring a goal in a friendly match against El Ahly. The match ended with a 4–0 win for Barcelona.

2007–08 season
On September 16, 2007, Bojan made his official debut for FC Barcelona against CA Osasuna, coming on at the 78th minute for Giovani dos Santos. Three days later, he made his UEFA Champions League debut against Olympique Lyonnais, coming on at the 88th minute for Lionel 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 October 2, coming on at the 81st minute for Ronaldinho against VfB Stuttgart.

On October 20, 2007, 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 April 1, 2008 against Schalke 04, netting the only goal in the first (away) leg of the quarterfinals, making him the first person born in the 1990s to score in the Champions League and the second youngest player ever, behind Ghanaian forward Peter Ofori-Quaye, then playing for Olympiakos CFP, who scored at the age of 17 years and 195 days.

Bojan finished the season with a record of 10 goals, breaking Raúl's record of most goals scored in a debut season.