Ljuboja was born in Vinkovci, SR Croatia, SFR Yugoslavia to Serb parents.
There he played in the youth teams of NK Dinamo Vinkovci, NK Osijek and Red Star Belgrade.
He moved to France where his professional career started with Sochaux in the 1998–99 season.
Ljuboja made his debut, coming on as a substitute in the 76th minutes for Anthony Sirufo, in a 2–1 loss against Lyon on 11 September 1998; then on 31 October 1998, Ljuboja scored his first goal and scored another, in a 4–0 win over Montpellier.
However, in his first season, Sochaux was relegated to Ligue 2.
The next season, Ljuboja soon became an important member of the first team and began his goalscoring form, including a hat-trick in a 5–1 win over Créteil on 15 April 2000.
At the end of the season, Ljuboja's goalscoring form led him to become a top-scorer for the club, but he was second top-scorer behind Amara Traoré.
However, the club wasn't able to return to Ligue 1, having come one point too short.
In his two-year stint with the team, he played 62 games scoring 20 goals.

Following his stay with Sochaux, Ljuboja moved to Strasbourg in the  2000–01 season.
In his first season, he made a slow start, scoring three goals in thirty appearances.
The club was relegated despite winning the Coupe de France final, beating Amiens 5–4 on penalties.
Soon in his second season, Ljuboja was able to bounce back, scoring fifteen goals and the club to return to Ligue 1.
He also made two appearances in the UEFA Cup competition, scoring twice against Belgian side Standard Liège but the club was knocked out, having lost 2–0 in the first leg.
Strasbourg was explained, due to winning the Coupe de France, the previous season.
The next season, in which the French League was renamed to Ligue 1, Ljuboja's goalscoring form soon faded, with nine goals but the club still remained in Ligue 1.
The season after, Ljuboja soon formed an important strike partnership with newly signing Mamadou Niang, which was short-lived as he moved from Strasbourg to PSG.
Because of his departure, Niang didn't score again for the remainder of the second half of that season.
Upon his departure, Ljuboja had made 123 league appearances scoring 34 goals in total.
In December 2003, Ljuboja was linked with Ligue 1 rival Paris Saint-Germain and two unknown Premier League clubs.
Ljuboja was born in Vinkovci, SR Croatia, SFR Yugoslavia to Serb parents. There he played in the youth teams of NK Dinamo Vinkovci, NK Osijek and Red Star Belgrade. He moved to France where his professional career started with Sochaux in the 1998–99 season. Ljuboja made his debut, coming on as a substitute in the 76th minutes for Anthony Sirufo, in a 2–1 loss against Lyon on 11 September 1998; then on 31 October 1998, Ljuboja scored his first goal and scored another, in a 4–0 win over Montpellier. However, in his first season, Sochaux was relegated to Ligue 2. The next season, Ljuboja soon became an important member of the first team and began his goalscoring form, including a hat-trick in a 5–1 win over Créteil on 15 April 2000. At the end of the season, Ljuboja's goalscoring form led him to become a top-scorer for the club, but he was second top-scorer behind Amara Traoré. However, the club wasn't able to return to Ligue 1, having come one point too short. In his two-year stint with the team, he played 62 games scoring 20 goals.
Following his stay with Sochaux, Ljuboja moved to Strasbourg in the  2000–01 season. In his first season, he made a slow start, scoring three goals in thirty appearances. The club was relegated despite winning the Coupe de France final, beating Amiens 5–4 on penalties. Soon in his second season, Ljuboja was able to bounce back, scoring fifteen goals and the club to return to Ligue 1. He also made two appearances in the UEFA Cup competition, scoring twice against Belgian side Standard Liège but the club was knocked out, having lost 2–0 in the first leg. Strasbourg was explained, due to winning the Coupe de France, the previous season. The next season, in which the French League was renamed to Ligue 1, Ljuboja's goalscoring form soon faded, with nine goals but the club still remained in Ligue 1. The season after, Ljuboja soon formed an important strike partnership with newly signing Mamadou Niang, which was short-lived as he moved from Strasbourg to PSG. Because of his departure, Niang didn't score again for the remainder of the second half of that season. Upon his departure, Ljuboja had made 123 league appearances scoring 34 goals in total. In December 2003, Ljuboja was linked with Ligue 1 rival Paris Saint-Germain and two unknown Premier League clubs.
Danijel Ljuboja