Kraft made his debut for Bayern's reserve team in 2006, and played in their first game in the newly formed 3. Liga on 17 July 2008. From 2008 to 2010, he was third-choice goalkeeper for the senior team, behind Hans-Jörg Butt and Michael Rensing. Following Rensing's release in 2010, he was promoted to second choice, and he made his first-team debut at the beginning of that season, in the 2010 DFL-Supercup. On 23 November 2010 he made his debut Champions League match in Rome against AS Roma. Bayern lost 3–2 after going into half-time with a 0–2 lead. The young goalkeeper had a good start and made some outstanding saves. During the 2010–11 winter break, Bayern coach Louis van Gaal announced that Kraft would replace Hans-Jörg Butt as Bayern's first-choice 'keeper for the second half of the season. Kraft made his debut as Bayern's first-choice keeper in a 1–1 Bundesliga draw to VfL Wolfsburg. Kraft produced top performance with several impressive saves to help FC Bayern to a 1–0 win on 23 February 2011 in a round of 16Champions League clash against Inter Milan. However, the decision to replace Butt with Kraft earned the displeasure of the Bayern board, and contributed to Van Gaal losing his job: after an error by Kraft allowed Christian Eigler to score the equaliser in a 1–1 draw with Nuremberg. Van Gaal – who was already due to leave – was sacked early, and temporarily replaced by his assistant Andries Jonker. Jonker reinstated Butt at Kraft's expense in his first game in charge, and shortly afterwards it was announced that Kraft would leave the club at the end of the 2010–11 season. The following week, 2. Bundesliga champions Hertha BSC announced that they had signed a four-year deal with Kraft on a free transfer. He made 19 appearances for Bayern's first team.
Hertha BSC
On 1 July 2011, Kraft joined Hertha BSC, which was promoted to the Bundesliga along with FC Augsburg. On 16 October 2011, Kraft returned for the first time with Hertha back to his old club Bayern Munich which turned out to be a quite bitter reunion for Kraft; the Berlin club lost 0–4. Prior to the game, Kraft and two other members of Hertha were honored with a bouquet of flowers by the Bayern staff and the fans were chanting pro Kraft throughout the game. On 25 June 2020, Hertha BSC announced the departure of Thomas Kraft, along with Salomon Kalou and four other players. Kraft announced his retirement shortly after, citing health problems.
