The club was plagued by financial issues in the late 1970s, and then again in the beginning of 1990s. In 1993, Hannover came up with an remarkable run that led to winning the first DFB-Pokal and assist in putting the financial foundations right. This run saw them beat Bundesliga teams Borussia Dortmund, VfL Bochum, Karlsruher SC, Werder Bremen and Borussia Monchengladbach. In the process, they were the first team from the lower division to win the tournament. The cup winners' hero is goalkeeper Jorg Sievers who made two saves in the semi-final game went to penalties, before scoring the winner on his own time in the penalty area. In the final of the cup He saved two times when the game was also decided via penalties. The team's lowest point was after being relegated from Regionalliga Nord (III) to Regionalliga Nord (III) for two seasons between 1996 and 1998: the fact that their departure of the league took place in the year of their centennial resulted in them being a laughing stock in the eyes of fans of teams that were competing for a long time to follow.
Hannover had a fresh start with a brand new squad of eager youngsters with a lot of them going to the national team, including Gerald Asamoah, Sebastian Kehl and Fabian Ernst - or impress in the Bundesliga. 1996 returned to tier II play in 1998 and then returned to in the Bundesliga in 2002 following an all-time high of 75 points. Since their promotions, the club has been able to consolidate in the top division with a string mid-table finishes under the direction of various managers. Coach Dieter Hecking was appointed only a few weeks into the 2006-07 campaign following an unfun beginning with Peter Neururer, in which the club was defeated in the three first games by a total of 11 goals. The 2007-08 season displayed some early signs of promise, with impressive pre-season victories against Rangers in addition to Real Madrid. However, they got inconsistent results during their first six Bundesliga games. The team put together an impressive three-match winning streak which culminated in the 2-0 victory over the champions VfB Stuttgart, to surge into the top six. After the break in winter, Hannover slipped after putting up some poor performances, but were redeemed to lose only twice in their final eleven matches during the campaign. They set a new record for points of 49 points for Die Roten in the Bundesliga and put the season in eighth position.
The 2008-09 season began badly for Hannover with defeats. But, it appeared to be rectified by the 5-1 win over Borussia Monchengladbach, a shock 1-1 win against Bayern Munich at home, which was not seen in twenty years and an exciting victory of 3-0 against Hamburger SV. Hannover found itself in the lower mid-table up to the break in winter. The second portion of the season was comprised of mixed results, depending heavily on home form in order to maintain Hannover within the elite division. The club eventually scored an away win with couple of games left, which helped to lift their spirits and stabilized their performance which led to an 11th-place final. The season was marked by uneven performance and numerous injuries to the key players.
The 2009-10 season began with renewed enthusiasm, with a brand new kit launched that featured traditional away kits as well as alternatives kits. Hannover also appointed an experienced technical director, Jorg Schmadtke. He provided a fresh perspective for the team. The new signings included Karim Haggui as well as Constant Djakpa, both from Bayer Leverkusen, Valdet Rama from FC Ingolstadt. The season began badly with a 1-0 defeat to Hertha BSC, and an unsatisfactory home draw against Mainz 05, after which coach Dieter Hecking quit the club in a voluntary manner. He was replaced by former coach Andreas Bergmann. The season was not over the team once more Hannover was plagued by important players injured, including many attacking players as well as crucial defenders, as being the tragic and shocking loss that took the life of German goalkeeper Robert Enke. Andreas Bergmann was removed as coach and was replaced by Mirko Slomka just after the break. Arouna Kone, and Elson were added to the team. Hannover 96 was for the most part of the season in area of relegation. With some victories in the final games of the season Hannover was required to win to be hopeful that the results would go their way for them. Hannover was able to win 3-0, with Arnold Bruggink, Mike Hanke and Sergio Pinto all scoring to keep them in the Bundesliga.
For the season 2010-11, Hannover stunned everyone by finishing a record fourth position, and getting into Europe at the 19th time. In 2011, the team started the season with a 2-1 victory over 1899 Hoffenheim before an away victory of 2-1 against 1. FC Nurnberg. In the play-offs of the Europa League, Hannover won against Sevilla 3-1 to advance to in the final group phase. Just before the close of the 2011-12 season Hannover Tech Director Jorg Schmadtke left the club due to issues with his family. There was speculation that Schmadtke was to join 1. FC Koln, but according to Bild, Schmadtke agreed with the president Martin Kind on a return to Hannover following his absence.
Hannover was a bottom team in the Bundesliga in 2015/16, and was dropped to 2. Bundesliga. The club decided to retain most of the first team together. But, following a positive beginning to the 2016/17 season however, a dip in results prompted the club's board to fire director Daniel Stendel, and appoint Andre Breitenreiter as their new manager. The team was able to score seven wins over the course of 11 games, which helped the 96ers finish in second place in the table behind VfB Stuttgart and bounce back to the top of the table in the first go-round.
The club was the subject of negative publicity after a large number of ultras traveled to England to play a preseason 2017/18 match against Burnley. They created troubles in the town center before the game. After entering Turf Moor they responded to an incident in the stadium within 40 minutes, by attacking the fans of the home team, breaking away seats and making them into missiles. According to police, the game was stopped at the half-time mark when Hannover being beaten 1-0 by Hannover.