On the eve of the German invasion Scheinboim was living in Lodz. When the invasion began, he transferred movement members from the German-occupied areas to Vilna. In November 1940 he married Pesia Zlotnik. In the Vilna ghetto he worked as an electrician in a Wehrmacht factory and sabotaged German equipment to the best of his ability.
In early 1942, an underground group under the command of Yechiel Scheinboim was established and began obtaining weapons from the Lithuanians and smuggling them into the ghetto with the help of members of the underground who were in the Jewish Police.
We considered leaving the Vilna ghetto and going to Bialystok, perhaps there we would succeed in organizing [resistance to the Germans]… We weighed up where to assemble the healthier youth in order to establish some form of defense, some form of uprising… There was not a single meeting, in which we did not deliberate how to reach a state of readiness for self-defense.
Elchanan Magid, The Second Struggle Group: Stories of Fighters from the Vilna Ghetto, interviewed and edited by Zvika Dror, p. 20 (translated from the Hebrew)
At the beginning of 1943, Scheinboim's group combined with Borka Friedman's "Struggle Group" to form "Yechiel's Struggle Group", which numbered some 200 members. They wanted to leave for the forests and to fight the Germans from there.
In May 1943 Yechiel's Struggle Group joined the FPO as an independent unit, represented by Yechiel Scheinboim in the FPO Staff Command. The two organisations did not combine forces, but the coordination and cooperation between them intensified.
On 1 September 1943, the ghetto was surrounded by Germans, Ukrainians, Lithuanians and Estonians. The Jews were forbidden from leaving for work. The Germans entered the ghetto and a group of underground members under the command of Yechiel Scheinboim opened fire on them. Yechiel was killed in the crossfire. Following this Aktion, the FPO abandoned the idea of an uprising since the rest of the ghetto inhabitants had not joined them, and members of the underground began leaving the ghetto for the Rudniki and Narocz forests. Members of Yechiel's Struggle Group also escaped from the ghetto to the forests, where they established units of Jewish partisans.
Yechiel was buried at the old Jewish cemetery in Vilna - the burial site of the "Vilna Gaon". His wife survived the Holocaust.