At the time that Werner was born his father was about to progress from being a school teacher of classical languages to being appointed as a Privatdozent at the University of Würzburg. Anna's father, Nikolaus Wecklein, was the headmaster of the Maximilians Gymnasium in Munich and it was while August Heisenberg was a trainee teacher at that school that he had met Anna. August and Anna were married in May 1899. Werner had an older brother Erwin, born in March 1900, who was therefore nearly two years older than the subject of this biography.
Sa oras na Werner ay ipinanganak ang kanyang ama ay tungkol sa progreso mula sa pagiging isang guro ng mga pangunahin wika sa pagiging hinirang bilang isang Privatdozent sa University of Würzburg. Anna's ama, Nikolaus Wecklein, ay ang punong-guro ng Maximilians himnasyo sa Munich at ito ay habang August Heisenberg ay ang itinuturo ng guro sa paaralan na na niya matugunan Anna. Agosto at Anna ay kasal sa May 1899. Werner nagkaroon ng isang mas lumang mga kapatid na lalaki Erwin, ipinanganak sa Marso 1900, na sa gayon ay halos dalawang taon na mas matanda kaysa sa paksa ng buhay na ito.