While in the occupation's carceral system, Yahya al-Sinwar headed the Supreme Leadership Committee for Hamas Prisoners for two organizational terms. He worked with fellow prisoners to organize and lead mass hunger strikes and protests, most notably in 1992, 1996, 1999, 2000, and 2004. Their demands included better detention conditions, an end to solitary confinement, family visits, and permission to receive newspapers and listen to the radio. Through their efforts, they were successful.
Al-Sinwar sustained resistance operations while imprisoned, including against prison. He and his comrade Ruhi Mushtaha retaliated against the Ramla prison warden’s mistreatment of Palestinian prisoners by throwing hot water on him. Al-Sinwar instructed his comrades to apply soap and oil on the floor to impede the guards' advance, such that they struggled to run on the slippery surface. On several occasions, he and his fellow prisoners carried out stabbing attacks against the guards.
From behind the high walls of Hadarim Prison, al-Sinwar also planned operations to kidnap occupation soldiers for exchange with Palestinian prisoners. According to former Shin Bet official Yossi Amrosi, al-Sinwar "directed a cell that sought to kidnap a soldier and smuggle him into Egypt through a tunnel in Rafah."