Recently, the there have been some bright spots for the team. have been a steady string of international appearances as part of the UEFA Cup and the UEFA Champions League beginning with the 1999 season. In addition, the signing of important players like Pal Dardai in 1997 , who became Herta's top capped player of all time, Sebastian Deisler in 1999 and Brazilian international Marcelinho in 2001 which won the league's player of the year award in the 2005 season. Hertha has also made a significant investment in its own youth soccer academy that has produced a number of players who have Bundesliga potential.
The team almost went down during the 2003-04 season but they rebounded and came in fourth in the following season however, they missed out on winning the Champions League after they were held to a draw the day of finals by Hannover 96. This saw Werder Bremen overtake them for the title on the day of the final league game. (As as a "thank-you" gesture Werder offered the Hannover team 96 champagne bottles.) In 2005-06, Herthaner was ranked sixth and then was selected to play in the UEFA Cup after defeating FC Moscow in the UEFA Intertoto Cup. Then, Hertha was eliminated in the opening round of the UEFA Cup by Odense BK. For 2006-2007, Hertha finished tenth after the sacking of coach Falko Gotz on April 11th. Hertha began the 2007-08 campaign with the new director Lucien Favre, who had been the winner of his first Swiss champion in the 2006 as well as 2007 for Zurich. Hertha was ranked tenth in the same league however, they were able to start the first qualifying stage of the UEFA Cup via the UEFA Respect Fair Play ranking which took them even further than an initial stage in the competition. After a very successful campaign in 2008-09, which saw them finish fourth and being within the race for the championship to the final day of the match, Hertha suffered an awful season in 2009-10, finishing second in Bundesliga and experiencing relegation.
After spending the entire 2010-11 season within the second. Bundesliga, Hertha secured its return to the Bundesliga in 2011-12 when it won by 1-0 against MSV Duisburg with three matchdays remaining during the season. Hertha was, however, placed sixteenth overall in 2011-12 Bundesliga and was beaten in the playoff for relegation to Fortuna Dusseldorf to fall back to the 2. Bundesliga.
The 2012-13 season was when Hertha gained promotion to the 2nd division to champions for the third time in the span of three seasons. On the first day of 2013-14's campaign, Hertha beat Eintracht Frankfurt 6-1 at the Olympiastadion to finish top of the Bundesliga table at the conclusion of matchday 1.
On February 5, 2015 Pal Dardai Hertha's longest-serving and the most captained player of all time with 366 appearances was appointed as manager of the main team. The halfway point of the 15-16 Bundesliga season Hertha was in 3rd in the table, which was its highest ranking during the break in the winter months since the 2008-09 season. Despite a slowing in the second half of the season, Hertha still finished in seventh place during the season which was the highest position within the Bundesliga since 2008-09 when Hertha was fourth. The seventh place finish ensured that Hertha was guaranteed Europa League football for the 2016-17 season as a result of a third-round play-off. Hertha fell in their third round playoff 3-1 in average to Brondby and won the first match with a 1-0 win at Berlin however losing in the following home tie 3-1. Teemu Pukki scoring a hat trick for the Danish team.
The year 2016-17 Bundesliga season Hertha had the best start ever to the Bundesliga season, in terms of points earned in the initial eight games, only losing one game - away to Bayern Munich - and forcing to draw with Borussia Dortmund. The 2017 Bundesliga holiday break Hertha was in third position in the league with nine wins with three draws, and four loss. Hertha ended the season in 6th position and was able to participate in their 2017-18 Europa League. Their spot on the team stage was confirmed on May 27, 2017 following Borussia Dortmund defeated Eintracht Frankfurt in the 2017 DFB-Pokal final.