After completing his secondary education at the gymnasium, Prützmann became a member of the Freikorps "Aulock" between 1918 and 1921, seeing active service in the Upper Silesian uprisings in the summer of 1921.

He would continue to serve in the Reichstag until the end of the Nazi regime, and he would successively represent East Prussia, Württemberg and Hamburg, as his SS postings changed.

When the post of Höherer SS- und Polizeiführer (HSSPF), (Higher SS and Police Leader) "Nordwest" (renamed "Nordsee" 20 April 1940) was created on 28 June 1938, Prützmann became the first holder of this position.

Immediately after the German invasion of the Soviet Union, he took up the position of HSSPF "Ostland und Rußland-Nord" (Baltics and Northern Russia) in Riga on 29 June 1941.

In this position, he was responsible for internal security and combating partisans in the Army Group North Rear Area encompassing the Baltic States and western Belorussia.

[7] In early 1942, Prützmann was put in charge of securing forced labor for the Durchgangsstrasse IV, a large project to build a road from Lemberg (now Lviv) to Stalino (now Donetsk).

[9] The next major advancement in Prützmann's career came on 29 October 1943 when he was named to the new post of Höchster SS- und Polizeiführer (HöSSPF), (Supreme SS and Police Leader) "Ukraine," one of only two officers to attain this designation, the other being SS-Obergruppenführer Karl Wolff in Italy.

[10] From June to November 1941, Prützmann held the post of HSSPF in the Baltic States under Hinrich Lohse, who was in charge of the Reichskommissariat Ostland.

One group, consisting mainly of civilian Nazi Party administrators headed by Lohse, and backed by Alfred Rosenberg, the Reichsminister for the Occupied Eastern Territories, wanted to confine the Jews to ghettos, confiscate all their property and work them as slave laborers in support of Germany's war effort.

[12] By the time Jeckeln took over as HSSPF, massive numbers of Jews had already been killed under Prützmann's administration, including those in the early Liepāja massacres.

[12] When Prützmann arrived in Ukraine in November 1941, mass murders of Jews and other Ukrainians had already been underway since shortly after the German invasion in June.

As Red Army advances on the eastern front pushed the German forces out of Ukraine, he moved back to Königsburg where he was still the titular HSSPF, though others had acted on his behalf during his long assignment in the Soviet Union.

[16] As originally conceived, the Werwolf units were intended to be legitimate uniformed military formations trained to engage in clandestine operations behind enemy lines in the same manner as Allied Special Forces such as commandos.

Some sources incorrectly give 21 May as his date of death, but 16 May is documented by the contemporaneous diary entry of British Major Norman Whittaker who was present at Lüneburg.