In 1998, Berlin was announced as the newest team to be added to the NFL Europe League. In cooperation with the B.Z., Berlin's best-selling newspaper, and Radio Energy 103.4, the people of Berlin chose the name of the team, 'Berlin Thunder'.
The Thunder made a slow start to life in the NFL Europe League, opening the 1999 season with four losses before NFC Pro bowl kicker David Akers (Philadelphia) landed a 33-yard overtime field goal in the Jahnstadion to record a first franchise win, 22-19 against Amsterdam. Head coach Wes Chandler's team finished the campaign with a 3-7 record. Chandler moved on to become wide receivers coach of the Dallas Cowboys in the off-season.
In 2000, new head coach Peter Vaas arrived from Barcelona Dragons and kept Thunder in the World Bowl race until late in the campaign. Despite failing to reach World Bowl, the Thunder finished the season with a 4-6 record and proved they were heading in the right direction.
Berlin Thunder crowned a successful 2001 season with victory in World Bowl IX when on June 30 the 8-2 Barcelona Dragons were beaten 24-17 in the Amsterdam ArenA. Quarterback Jonathan Quinn led his team to a 6-4 record despite a slow start that included two losses in the first three games. The World Bowl berth was secured with a 34-28 victory in week 10 in Amsterdam. Quinn was fittingly named MVP of World Bowl IX and was also named to the All-League team having played a dominant role throughout the season, passing for a team-record 24 touchdowns, the second-most in NFLEL history.
In 2002, the Thunder made a slow start to their title defense, dropping the opening three games of the year. They rallied down the stretch with offensive stars quarterback Todd Husak, running back Anthony White who joined the team from week 4 and wide receiver Dane Looker leading the way to compile a 6-4 record - good enough for a berth in World Bowl X. Going into the Championship Game as the hottest team in the league, Berlin recorded a 26-20 victory over the hometown Rhein Fire in the final NFLEL game played at Düsseldorf's Rheinstadion.
Victory meant Berlin became the first team to go 0-3 and win a World Bowl and also became the first club to win back-to-back championships.
In 2003, Berlin Thunder was looking for the third straight title in "Mission threepeat". The move to Berlin's famous Olympic Stadium gave the Thunder a new attendance record with 16,312 spectators in the very first game versus Rhein Fire and a new overall record with 12,238 per game. On the field there wasn´t as much success and the Thunder finished the campaign with a 3-7 record.
The 2004 season was the most successful in club history with new head coach Rick Lantz guiding his team to an NFL Europe League-best 9-1 regular season record, culminating in a 30-24 defeat of the Frankfurt Galaxy in World Bowl XII. By winning their third league title in four years, the Thunder joined Frankfurt as the only team to win three World Bowls.
In 2005, Berlin won seven games and became the first team in league history to repeat as regular season champions. Their 16 wins in 2004 and 2005 were a league record for a two-year span. The 2005 campaign also saw Berlin break its attendance record as 20,927 fans saw the Thunder take on the Cologne Centurions in Week 10. But the season ended in disappointment as the Thunder fell to a 27-21 defeat at the hands of the Amsterdam Admirals in World Bowl XIII. The 2006 season proved to be Lantz's final campaign in Berlin as the Thunder finished bottom of the standings with a 2-7-1 mark. Lantz joined the Rhein Fire in January, 2007, while John Allen was unveiled as the fourth head coach in team history.