The history of the Tohoku Rakuten Golden Eagles Nippon Professional Baseball (NPB) began in 2004 when two Pacific League (PL) teams, the Osaka Kintetsu Buffaloes and the Orix BlueWave, merged to create the Orix Buffaloes. After the league's first and only players strike on September 18–19, team representatives agreed to ease the rules of entry for new teams into NPB and that one would be allowed to join the following season to fill the void left by the merger. Beating out Livedoor, Hiroshi Mikitani's internet services company Rakuten was selected to create a new PL team to be based in Sendai, Miyagi Prefecture. The new club was named the "Tohoku Rakuten Golden Eagles" and they would play in the newly renovated Miyagi Stadium.

2004: Origins and formation

In June of Nippon Professional Baseball's (NPB) 2004 season, the Osaka Kintetsu Buffaloes and the Orix BlueWave announced that, due to financial difficulties, the two teams planned to merge into one for the start of the 2005 season. Both teams were in the Pacific League (PL), and a merger between the two would result in a team imbalance with the PL's opposing league, the Central League (CL). As a large number of players were expected to lose their jobs when the merger was finalized, the Japan Professional Baseball Players Association (JPBPA) organized a players' strike in an attempt to force the postponement of the merger for at least one year. When team officials definitively announced that a one-year freeze on the merger was impossible, the players conducted a two-day strike on September 18–19, 2004. With the threat of further strikes looming, team representatives agreed to ease the rules of entry for new teams into NPB and that one would be allowed to join the following season.

That same month, Takafumi Horie, president of the internet services company Livedoor, established a new professional baseball team and applied for team ownership with NPB, hoping to fill the void left by the merger of the BlueWave and the Buffaloes. Horie intended the team to be composed of players who were left jobless after the merger and planned for it to be based in Sendai, Miyagi Prefecture. One week later a second internet services company, Tokyo-based Rakuten, also submitted a formal application to Japanese professional baseball to form a team. Like Horie, Rakuten president Hiroshi Mikitani also expressed a desire to locate his new team in Sendai.

In early October, the public screening process to select one of the two companies and allow them form a new NPB team began. Both Livedoor and Rakuten were given an hour and a half to discuss their team and budget propositions before a panel of five Japanese baseball executives. The panel consisted of Central League chairman Hajime Toyokura and the head officials of the Yomiuri Giants, the Yokohama BayStars, the Seibu Lions and the Chiba Lotte Marines. The screening standards included the adequacy of the applications, the prospective continuity and stability of the planned baseball teams, the prospective financial standings of the applicants and planned teams, and their planned baseball facilities. As screenings were held weekly through October, more details about each potential new team emerged. Rakuten, announced Marty Kuehnert and Yasushi Tao as general manager and manager, respectively, of their newly named "Tohoku Rakuten Golden Eagles" baseball club. The team was named after the Japanese golden eagle, a large, endangered, predatory bird found in the mountains of the Tōhoku region. Upon registering the trademark for their name, Rakuten learned that Livedoor had registered an "eagles" trademark one day earlier. Livedoor allowed Rakuten to use the name, however, after it placed second behind "phoenix" in an internet poll that the company was using to determine the name of their team.

A telephone survey conducted by Kyodo News during the selection period of 300 people living in Tōhoku indicated that Livedoor was the early fan favorite to win the right to start a new team in Sendai. In the survey, forty percent of the respondents supported Livedoor's bid compared to only seven percent supporting Rakuten. Rakuten, however, was considered the more likely of the two companies to be chosen by NPB. Rakuten president Mikitani had extensive connections in established Japanese business circles and already operated another sports team, the soccer club Vissel Kobe in Japan's J.League. On November 2, NPB selected Rakuten over Livedoor to create a new Pacific League team to be based in Sendai. The team would play its home games in Miyagi Stadium, which was being renovated by Rakuten. It was the first time a new team, excluding cases of mergers or acquisitions, joined NPB since the creation of the now-defunct Takahashi Unions in the Pacific League in 1954.

Team owner Mikitani was looking for someone that didn't have a relationship with the old Japanese business community to run the team. In hiring Kuhnert, NPB's first foreign general manager, he hoped to bring "new blood" and "innovative ideas" to Japanese baseball. Kuhnert's approach to the team was analytic and sabermetrics-minded. He was known for his criticisms of Japanese baseball's traditionally intense training methods and hired a like-minded managers and coaches. The Eagles' budget for the year was $22 million, the lowest in NPB.

Instead of allowing the Eagles to draft players from all 11 NPB teams in an expansion draft, the team had to construct their roster from the 107 players left over from the dissolved Kintetsu and original Orix teams during a special dispersal draft held on November 8. Furthermore, Orix was allowed to select 25 players that would be protected from the distribution process before the draft, thus giving them preferential signing rights. Included in these selections were all free agents and foreign players. Rakuten was only then allowed to select 20 unprotected players, not including any first- or second-year players. After that, the first- and second-year players were unprotected and Orix and Rakuten alternating selecting 20 more players for the last round of the draft. Of the 40 players the Eagles selected, 17 were pitchers and 23 were position players. The league's decision to employ an unequal dispersal draft to build the Eagles roster was blamed for the team's struggles to come. An expansion draft would have better allowed for the new team to be more competitive. Mikitani believed the draft to be "unfair".

In the draft, Rakuten was able to pick up former Buffaloes outfielder Koichi Isobe. Isobe was left unprotected by Orix as he refused to play for their newly formed team because of their involvement in the merger. Despite also voicing that he no intention of playing for the merged team, Orix protected Hisashi Iwakuma, the Kintetsu Buffaloes' pitcher who led the league in wins the previous season. Iwakuma insisted that Orix team president Takashi Koizumi live up to his pledge that he would sincerely listen to the players involved in the merger regarding their futures. After four rounds of talks between Iwakuma and Koizumi, negotiations broke down and the JPBPA was brought in to mediate. Eventually, Orix agreed to trade him to the Eagles in exchange for cash. Rakuten also signed five foreign players before the start of the season to help fill out its debut-season roster.

2005–2009: Debut and the road to the Climax Series

After winning the first game of their debut season behind starting pitcher Hisashi Iwakuma, the Tohoku Rakuten Golden Eagles lost their second game to the Chiba Lotte Marines, 0–26. The loss tied the 1946 Gold Star record for losing by the highest run differential in Japanese professional baseball history. Following a 6–22 start, just over a month into the season, the Eagles removed Kuehnert as general manager and demoted the head and batting coaches. Eventually it was revealed that there had been friction between Kuehnert and higher-ups, and that he had been denied powers afforded to most general managers, such as being able to attend league or players' association meetings, having input in the budget, and being made a company director. Over the course of the season, the team posted two separate 11-game losing streaks and last place in the PL was ensured after a loss on August 29, a month before the end of the regular season. The Eagles finished 51.5 games out of first place and was the first NPB team in 40 years to lose over 90 games in a single season. As a result, ten players were released, and Tao was dismissed despite being signed to a three-year contract.

In an otherwise disastrous season, one highlight was team's home debut on April 1. Only five months after being awarded a franchise and without a preseason game as a dry run, Rakuten ran and operated the game smoothly in front of a packed, newly named Fullcast Stadium. Isobe hit a home run in the team's first at-bat, and they went on to defeat the Seibu Lions, the defending Japan Series champion, 16–5. It was also estimated that the economic impact of the team in the Tōhoku region was $300 million in the first year. Furthermore, after the season, the team expected to post a profit of tens of millions of yen instead of the ¥1.5 billion loss that it had projected. Contributing factors were that the average home-game attendance for the year came close to the team's target of 15,000 per game, sales of Eagles' merchandise were strong, and players' performance-based pay was minimal. The team expected to post a loss the next season with plans to spend more than ¥1 billion on enhancing player training and about ¥3 billion on the continuing remodel of Fullcast Stadium. The stadium's off-season renovations expanded its seating capacity to allow for 23,000 spectators in addition to adding a sports bar, press seats, broadcast booths, a lounge, luxury boxes, and additional food concessions.

In an about-face from its nontraditional approach to its inaugural season, Mikitani instead looked to experience to lead the Eagles in its second season when he replaced first-time manager Tao with Hall of Famer and veteran manager Katsuya Nomura. The team also acquired third baseman José Fernández from the Seibu Lions in the off-season. The team improved slightly over its first season, and Fernández went on to receive the Eagles' first Best Nine Award in his first season with the team. However, the 2006 season also brought the Eagles' their first no-hit loss, and they still finished last in the Pacific League. At the end of the season, Rakuten drafted pitcher Masahiro Tanaka in the first round of the 2006 amateur high school draft. They were awarded the opportunity to draft Tanaka after winning a four-team lottery against the Yokohama BayStars, Orix Buffaloes, and Hokkaido Nippon-Ham Fighters, who also named him as their first-round selection.