Spektor died at Kovno on 6 March 1896. Various institutions were named after him, including Rabbi Isaac Elchanan Theological Seminary (RIETS, part of Yeshiva University) and the Knesses Beis Yitzchok Kaminetz of Baruch Ber Leibowitz. He had three sons: Chayyim, who was the son-in-law of R. Joseph Böhmer of Slutzk, and died in Kovno in 1874, aged forty; Benjamin Rabinovich; and Hirsch Rabinovich, who was "maggid" or preacher of Wilna, and later succeeded his father as rabbi of Kovno. An only daughter, named Rachel, died at an early age in 1876.