In the new millennium, Dinamo Zagreb continued to land more trophies, winning at least one domestic competition per season, save for 2004–05, when they were knocked–out of the Croatian Cup and finished seventh in Prva HNL.
After the 1999–2000 title-winning campaign, Dražen Ladić, Goran Jurić, Robert Prosinečki, Tomislav Rukavina, Krunoslav Jurčić, Daniel Šarić and Igor Bišćan all either left the club or retired and were replaced by a new generation of players, including Luka Modrić, Eduardo, Vedran Ćorluka, Niko Kranjčar, Mario Mandžukić, Ivica Olić, Tomislav Butina, Dino Drpić, Boško Balaban, Tomislav Šokota, Ivan Turina, Dario Zahora, Mihael Mikić, Danijel Pranjić and Ivan Bošnjak, among others.
[1] The newly renamed club won their fifth consecutive title, by a large margin of 14 points ahead of Hajduk Split in the 1999–2000 season.
After being knocked out of the Champions League qualifiers by Milan (with Andriy Shevchenko scoring four goals in two matches against them), Dinamo continued their European season in the UEFA Cup.
In the championship playoffs, Hajduk Split, who initially sat in third, finished at top of the table, securing their fourth league title, just one point ahead of Dinamo.
The 2001–02 season started well for Dinamo, as they were through the UEFA Cup qualifying rounds, defeating Flora Tallinn 1–0 in both home and away matches.
After a series of poor results, club manager Ilija Lončarević was sacked and the newly employed was Marijan Vlak, who had previously served in the role.
He loaned in Balaban from Aston Villa and bought the top goalscorer of the previous Prva HNL season, Ivica Olić, from NK Zagreb.
It would prove to be a great transfer deal for Dinamo, as Olić finished the season with 16 league goals, retaining the top goalscorer title.
Nonetheless, Blažević did manage to secure the Croatian Supercup title against Prva HNL title-holders NK Zagreb.
After two seasons, Dinamo was back on top as they won their seventh league title with eight points ahead of runners-up Hajduk Split.
Later signings, experienced strikers Veldin Karić, Mladen Bartolović and Zoran Zekić, had even lesser impact on team's overall performance.
The run continued with two wins against rival teams Slaven Belupo and Varteks, but was again abrupt by a goalless draw against Hajduk Split at the Maksimir.
Since Dinamo did not take part in any European competition and was eliminated early in the Croatian Cup, the squad was able to fully devote themselves to the Prva HNL matches, and it saw the team top the league with an 11-point margin over the second placed Rijeka after the season's initial 22 rounds.
Dinamo continued to dominate in the championship playoffs and secured their eight league title in front of the runners-up Rijeka and third-placed Slaven Belupo.
He enjoyed a good start into the new season as he won the Croatian Supercup defeating Rijeka 4–1 and reaching the third qualifying round of the Champions League.
He also recorded two home wins at the start of the 2006–07 Prva HNL campaign before the club was to face English side Arsenal in the Champions League.
The first team squad has seen some major changes in the new season, as the top goalscorer Eduardo had departed to Arsenal for a £7.5 million transfer fee and was replaced by young striker Mario Mandžukić, who was brought to Maksimir from city rivals NK Zagreb.
[2] The club had also signed experienced German goalkeeper Georg Koch, centre-back Gordon Schildenfeld, Ivorian midfielder Did'dy Guela and former star striker for Dinamo, Boško Balaban.
The first leg was played at Maksimir, a match which Dinamo lost narrowly after Schildenfeld made fatal back-pass which allowed the away team to score for a 1–0 victory.
The club also won the 2008–09 Croatian Cup after defeating Virovitica, Šibenik, Slaven Belupo, NK Zagreb and Hajduk Split.
A major changes were made in the senior squad, with number of important first-team players being sold to top-flight European teams.
Dinamo continued their European season in the first round of UEFA Cup, being drawn against Czech side Sparta Prague.
During the winter transfer window, Dinamo signed centre-back Robert Kovač, strikers Ilija Sivonjić and Miroslav Slepička, as well as Argentine defensive midfielder Adrián Calello.
Jurčić also led the club to their tenth Croatian Cup title, defeating Hajduk Split after a penalty shootout at the Stadion Poljud.
In the 2009–10 season, Dinamo director of football Zoran Mamić announced that the club was determined to reach the group stage of the 2009–10 Champions League and some big signings were promised.
The club was successful to sign Greek striker Dimitrios Papadopoulos and full-back Leandro Cufré, who were arguably one of the best foreign footballers that played for Dinamo in recent years.
Although they lost 2–0 away at Tynecastle Stadium, the club secured place in the group stage draw of the first ever Europa League competition, after its rebranding from the UEFA Cup.
The first Croatian Cup title in new century came already in 2000–01 season, as Dinamo defeated their biggest rivals Hajduk Split 3–0 over two legged match, prevailing 2–0 at Poljud and 1–0 at Maksimir.
Since then, the club has entered all of the Croatian Cup competitions, winning the title on six occasions, the latest being in 2009 when they defeated Hajduk again, this time after a penalty shootout.