Borgmann began his career in the early 1980s, working mainly with the Berlin Art Ensemble with Nick Steinhaus (participating in the 1981 South American tour for the Goethe-Institut and the 1982 Nickelsdorfer Konfrontationen).
He went on to the Sirone Sextet in New York in 1987.
He also spent some time playing with the Hidden Quartet (with Dietmar Diesner, Erik Balke, and Jonas Akerblom), and the Noise and Toys (with Valery Dudkin, Sascha Kondraschkin).
In 1991 Borgmann founded the Orchestra Kith’n Kin, bringing together Hans Reichel, John Tchicai, Pat Thomas, Jay Oliver, Mark Sanders, and Lol Coxhill, amongst others.
A year later came Ruf der Heimat which included Ernst-Ludwig Petrowsky (Ruf der Heimat, 1995) and Peter Brötzmann (Machine Kaput, 1996, both Konnex). Borgmann has taken part in trio Blue Zoo, with Peter Brötzmann and Borah Bergman (Ride into the Blue 1996 and Blue Zoo 1997, both Konnex). Throughout 1984, and continuing until 1996, he also organized the STAKKATO festival in Berlin.

In 1995 Borgmann began working with Wilber Morris and Denis Charles, forming the BMC Trio. After Charles‘ death in 1998, Borgmann and Morris teamed with Reggie Nicholson creating the „BMN-Trio„, which continued performing until 2002. Borgmann also participated in the quartet Alliance with Ernst-Ludwig Petrowsky, DJ Jayrope, and Michael Griener.

Borgmann and Brötzmann meet the New York rhythm team of William Parker and Rashid Bakr on Cooler Suite (2003, Grob).

Initially teaming with Tony Buck, and Joe Williamson, Borgmann formed the trio Boom Box, releasing their album Jazz in 2011.
He continues to perform with the group, now playing with Willi Kellers and Akira Ando. He also continues to tour international Jazz festivals around the world.

During his career, Borgmann has taken part in concerts, tours, and recordings with artists including Peter Brötzmann, Borah Bergman, Paul Lovens, Tony Buck, Paul Lytton, Evan Parker, John Tchicai, Conny Bauer, Johannes Bauer, Charles Gayle, Heinz Sauer, Lol Coxhill, Phil Minton, William Parker, Jason Hwang, Thurston Moore, Shoji Hano, Alexander von Schlippenbach, Rashied Bakr, Roy Campbell, Perry Robinson, Kip Hanrahans Latin Groove, and Jean-Paul Bourelly.

Thomas Borgmann has twice been the recipient of the Berlin Jazz-Grant, first in 1994, and again in 1996.