After playing in the youth teams of Čelik Zenica, Krstajić moved to Kikinda, FR Yugoslavia, present day Serbia in April 1992, following the breakout of the Bosnian war. He started playing with Senta for six months. He then moved to OFK Kikinda, at that time a first league club. At some point of a successful career as a Serbian football player, there comes the time, to decide, whether one wants to play for Partizan or for Red Star Belgrade, and Krstajić decided to take the move to Partizan in 1996. According to Krstajić himself, Red Star was interested in him, but as he comes from a "Partizan" family, he decided to sign a contract with his favourite club. His four and a half years at Partizan were more than successful, winning the national championships three times and also the national cup in 1998.
In 2000, Krstajić, the defender with the "winner mentality" joined German Bundesliga club Werder Bremen who paid a DM 1.8 million transfer fee to Partizan. At Werder Bremen he was initially deployed at left-back in his first season but became one of the best central defenders in the Bundesliga, winning the German championship and the cup with Werder in 2004. In 2004 he joined Schalke 04, where he was named the new captain on 17 March 2009.
Partizan
On 5 June 2009, Krstajić signed a two-year contract with his former club Partizan. In January 2010, after the departure of Nenad Đorđević, he was named the new Partizan captain. After two very successful seasons, Krstajić played his last professional match on 21 May 2011. Immediately after retiring, he was appointed as the new director of football of the club. After less than 6 months as director of football, he was sacked due to a media war against club president Dragan Đurić. Aleksandar Stanojević resigned as manager as a result. The day before Krstajić was released, Partizan fans, Grobari, chanted his name as a sign of support during a basketball match against arch rivalsCrvena Zvezda.
International career
Krstajić was a part of the Serbia and Montenegro national team "Famous Four" defence, which conceded just one goal during the qualifying for the 2006 FIFA World Cup. The other members of the famous four were Ivica Dragutinović, Goran Gavrančić and Nemanja Vidić. Between 1999 and 2008 he made 58 international appearances scoring 2 goals. He represented three senior national sides: FR Yugoslavia, Serbia and Montenegro, and Serbia.
Managerial career
Serbia
In October 2017, Krstajić succeeded Slavoljub Muslin as head coach of the Serbia national team, initially as a caretaker. In December, it was announced he would take on the role permanently and at least until the end of the 2018 FIFA World Cup. On 13 June 2019, Krstajić was sacked from the position after a dismal 5–0 loss in a UEFA Euro 2020 qualifier against Ukraine.
Administrative career
Before becoming a manager, Krstajić became the new chairman of the board of Bosnian Premier League club Radnik Bijeljina on 23 January 2015. During his time as club chairman, Radnik became a stable Bosnian Premier League club, finishing almost always in the top five or six. It won its first ever national and major trophy, the Bosnian Cup in the 2015–16 season and thus qualified for its first ever UEFA competition, the 2016–17 UEFA Europa League qualifying rounds. In the 2018–19 Bosnian Premier League season, Radnik finished in fifth place, but as fourth placed Željezničar did not get an UEFA license to compete in the following season's UEFA Europa League, Radnik was qualified by default to the 2019–20 UEFA Europa League qualifying rounds for a second time in its history. On 27 December 2019, Krstajić unexpectedly decided to leave Radnik, stating that it was time for someone new to lead the club. He officially left the club on 28 March 2020, with Predrag Perković succeeding him as chairman.
