Dörner came late to the trumpet. Born in 1964 in Köln, Germany, he studied the piano, first at the conservatory in Arnhem, The Netherlands, in 1988-1989, and then at the Musikhochschule in Köln. In 1991, he picked up trumpet as a second instrument, studying with Malte Burba. Avant-garde jazz became an escape from academia. While in Köln he performed with Bruno Leicht as the Streetfighters. It is during that period that he formed his first group, the Axel Dörner Quartet with Frank Gratkowski, Hans Schneider, and Martin Blume, whom he would later join in the international free improv group Lines. He recorded his first session in 1993 with the Remedy, a trio with Sebastian Gramß and Claus Wagner.

In 1994, Dörner moved to Berlin and dove head first in the free improv scene there, leaving the piano behind. With saxophonist Rudi Mahall he started the Thelonious Monk tribute band Die Enttäuschung. The pair also joined old-school free jazz drummer Sven-Ake Johansson's group and later formed the Electrics. The trumpeter was drafted for Lawrence "Butch" Morris' Berlin Skyscraper tour of 1995, which led to friendships with musicians based in London and membership in the Chris Burn Ensemble. He also became a regular collaborator with Alexander von Schlippenbach. All the while he began to develop his new techniques, a hint of the process being illustrated by Claque (1998), his first album as a leader, recorded with Chicago improvisers Fred Lonberg-Holm and Michael Zerang. He had a chance to explore his newly found interest with the new music ensemble Zeitkratzer where he held a tenure for a short while (recording two discs with them) and applied it in small group improvisation with John Butcher and Xavier Charles in 2000-2001, a project that yielded the influential album The Contest of Pleasures (2001). Trumpet (2001), his first solo CD, shows how far he went with the concept of microscopic sound.