He was, from September 1932, a civilian cryptologist with the Polish General Staff's Biuro Szyfrów (Cipher Bureau), housed in the Saxon Palace in Warsaw.

He worked there with fellow Poznań University alumni and Cipher Bureau cryptology-course graduates Marian Rejewski and Jerzy Różycki.

In 2000 he was posthumously awarded by President Aleksander Kwaśniewski the Grand Cross of the Order of Polonia Restituta for his "outstanding contributions to the Republic of Poland".

[1] In 2009 the Polish Post issued a commemorative stamp featuring Henryk Zygalski alongside fellow cryptologists Marian Rejewski and Jerzy Różycki.

[2][failed verification] On 5 August 2014 the Institute of Electrical and Electronics Engineers (IEEE) honored Rejewski, Różycki, and Zygalski with its prestigious Milestone Award, which recognizes achievements that have changed the world.