The Pinkas Synagogue is dedicated to the Jewish victims of the Holocaust from Bohemia and Moravia; their names are inscribed on the walls of the main nave and adjoining areas. The interior of the synagogue comprises Memorial 77,297, which was designed and executed by the painters Václav Boštík (b. 1913) and Jiří John (1923-1972) between 1954 and 1959. The memorial was closed in 1968, however, since the building was in an increasingly poor state of repair. After remaining closed for a long time, the building was eventually reconstructed and, following the collapse of the Communist regime, a project was launched to renovate the memorial, which reopened in 1996.

The text of the inscriptions was compiled from card indexes, which were drawn up shortly after the war on the basis of extant transport papers, registration lists and survivor's accounts. The names of Holocaust victims, together with their dates of birth and death, are inscribed on all the interior walls. Where the precise date of death is not known - which is generally the case - the date of deportation to the ghettos and extermination camps in the east is stated instead - this is usually the last information we have on the victims. Their names are arranged according to the towns and villages where they were living prior to deportation or arrest and are presented in alphabetical order. The main nave features the names of people whose last address prior to deportation was in Prague; the rest of the interior space commemorates victims from towns and villages outside Prague.

On both sides of the Holy Ark (aron ha-kodesh) are recorded the names of some of the ghettos and camps where Bohemian and Moravian Jews were deported and, in most cases, exterminated. This memorial is a long epitaph commemorating the names of those for whom a tombstone could not be erected.