Ben-Ari grew up in the Kfar Shalem neighbourhood in south Tel Aviv, born to Mizrahi Jewish parents from Iran and Afghanistan. He studied at the Bnei Akiva yeshiva at Kfar Haroeh, at the hesder yeshiva in Yamit, and at the Mercaz HaRav yeshiva. As part of his hesder army service, he was with the Nahal settlement at Neve Dekalim from 1982 to 1986.