In total, the prison was the location for 5 executions between 1930 and 1938, when the democratic First Czechoslovak Republic ceased to exist following the Munich Agreement and German, Hungarian and Polish occupation of the country's border areas.

Thousands of Czech people, from members of the resistance to alleged black marketeers, were detained here before being sent to execution sites, especially the Kobylisy Shooting Range, to other prisons within Nazi Germany, or to concentration camps.

[3] In spring 1943, the Nazis started carrying out executions directly inside the facility itself, where three cells had been adapted for this purpose.

[1] General Josef Bílý, who at the beginning of the German occupation of Czechoslovakia led the anti-Nazi resistance group Obrana Národa ("National Defense"), was imprisoned at Pankrác Prison before being executed by shooting elsewhere in 1941.

[1][2][5][6] After the war, many executions of Nazi officials and collaborators took place in the prison, including the hanging of Karl Hermann Frank, as well as Kurt Daluege, the SS chief responsible for the Lidice and Ležáky massacres.

[1] In the 1960s, Czechoslovakia became the only country to the East of the Iron Curtain which accepted the United Nations standard minimum rules for prisons.

[11] During the week, convicted prisoners are involved in 40 to 50 activities whose purpose is to reduce tension and uncertainties which accumulate due to being imprisoned.

The convicts work in the framework of internal workplaces, e.g., such as KOVO, Printing office, Laundry, Maintenance, Automobile repair shops.

[12] In the prison, 9 educational, 22 special-interest (club-or hobby-oriented), and 14 special formative activities are organized for convicted inmates (not to those held on remand, though).

The goal of such program is the development of personality, enhancement of creativeness in purposeful uses of free time, and improvement in the involvement in civilian life of the convicts.

Although the principle of "not guilty until proven otherwise" applies, in reality the inmates held on remand face worse regime than those convicted, as they cannot take part in educational, sport or working activities, mostly because they are expected to be held only for a limited time (the average is approximately 100 days) before being either released or moved after the verdict.

According to Mindii Kašibadze, who spent two years in Pankrác on remand before the Czech courts eventually dismissed his Georgian international arrest warrant, the prison is infested with rats and has only "five cells of European standard which are a show case for outside visitors".

In such cases, the responsible judges from other districts come to conduct trial in the High Court's building, rather than detainees being transported to their courthouses.