
In September 1939, World War II began, and Stojaciszki was occupied by the Soviets. In 1940, when the Soviet Union annexed Lithuania, Stojaciszki was allotted to the "Lithuanian Soviet Republic." In June 1941, on the eve of the Soviet-German War, there were about 350 Jews in the village. The Germans occupied Stojaciszki in late June, several days after their invasion of the Soviet Union. In September 1941, the 300 remaining Jews of Stojaciszki were transferred to the nearby township of Hoduciszki, four kilometers southeast of Stojaciszki, where they shared the fate of the local Jews: In late September, the two groups were taken to the so-called "Poligon" near Nowe Święciany and killed there.
Stojaciszki was liberated by the Red Army in July 1944. Seven Jews from the village survived the war.
| Last Name | First Name | Year of Birth | Place of Residence | Fate |
|---|---|---|---|---|
| Abel | Bentzion | Stojaciszki, Poland | murdered | |
| Abel | Chaia | Stojaciszki, Poland | murdered | |
| Abel | Ester | Stojaciszki, Poland | murdered | |
| Abel | First name unknown | Stojaciszki, Poland | murdered | |
| Abel | Hade | Stojaciszki, Poland | murdered | |
| Abel | Idl | Stojaciszki, Poland | murdered | |
| Abel | Khloine | Stojaciszki, Poland | murdered | |
| Abel | Malka | Stojaciszki, Poland | murdered | |
| Abel | Shmuel | Stojaciszki, Poland | murdered | |
| Abel | Shose | Stojaciszki, Poland | murdered | |
| Abel | Tzerne | Stojaciszki, Poland | murdered | |
| Abel | Yaakov | Stojaciszki, Poland | murdered | |
| Abel | Yisrael | Stojaciszki, Poland | murdered | |
| Beigel | Ester | Stojaciszki, Poland | murdered | |
| Beigel | Leib | Stojaciszki, Poland | murdered | |
| Beigel | Pese | Stojaciszki, Poland | murdered | |
| Beigel | Reize | Stojaciszki, Poland | murdered | |
| Beigel | Shmuel | Stojaciszki, Poland | murdered | |
| Beigel | Szmuel | 1888 | Stojaciszki, Poland | murdered |
| Beigel | Yisrael | Stojaciszki, Poland | murdered | |
| Bejgel | Chaim Israel | 1916 | Stojaciszki, Poland | murdered |
| Epstein | Sara | 1900 | Stojaciszki, Poland | murdered |
| Faktor | Isak | 1912 | Stayetishkis, Poland | not stated |
| Faktor | Sora | 1913 | Stayetishkis, Poland | not stated |
| Gantovnik | Barukh Yitzkhak | Stojaciszki, Poland | murdered | |
| Gantovnik | Beile | Stojaciszki, Poland | murdered | |
| Gantovnik | Eliahu | Stojaciszki, Poland | murdered | |
| Gantovnik | First name unknown | Stojaciszki, Poland | murdered | |
| Gantovnik | Gdaliyahu | Stojaciszki, Poland | murdered | |
| Gantovnik | Ite Sheine | Stojaciszki, Poland | murdered | |
| Gantovnik | Khaim | Stojaciszki, Poland | murdered | |
| Gantovnik | Khiene | Stojaciszki, Poland | murdered | |
| Gantovnik | Meirim | Stojaciszki, Poland | murdered | |
| Gantovnik | Moshe | Stojaciszki, Poland | murdered | |
| Gantovnik | Rachel | Stojaciszki, Poland | murdered | |
| Gantovnik | Reuven | Stojaciszki, Poland | murdered | |
| Gantovnik | Sara | Stojaciszki, Poland | murdered | |
| Gantovnik | Shalom | Stojaciszki, Poland | murdered | |
| Gantovnik | Shimshon | Stojaciszki, Poland | murdered | |
| Gantovnik | Yisrael | Stojaciszki, Poland | murdered | |
| Gantovnik | Yisrael | Stojaciszki, Poland | murdered | |
| Gantovnik | Zlate | Stojaciszki, Poland | murdered | |
| Gantownik | Barukh Yitzkhak | 1885 | Stojaciszki, Poland | murdered |
| Gantownik | First name unknown | Stojaciszki, Poland | murdered | |
| Gantownik | First name unknown | Stojaciszki, Poland | murdered | |
| Gantownik | First name unknown | Stojaciszki, Poland | murdered | |
| Gantownik | Rejuwen | 1893 | Stojaciszki, Poland | murdered |
| Gantownik | Szara Bejla | 1875 | Stojaciszki, Poland | murdered |
| Gantownik | Szolem | 1880 | Stayetishkis, Poland | murdered |
| Gantownik | Zalman | Stojaciszki, Poland | murdered |