The NF-κB pathway is known to be involved in regulating apoptosis, inflammation and immunity in organisms. In this study, we first identified full-length cDNA sequences of two key molecules in the NF-κB pathway, namely, NEMO and p65, and characterized their responses in the hindgut of Urechis unicinctus (Echiura, Urechidae) exposed to sulfide. The full-length of cDNA was 2491 bp for U. unicinctus NEMO (UuNEMO) and 1971 bp for U. unicinctus p65 (Uup65), and both polyclonal antibodies were prepared using UuNEMO or Uup65 expressed prokaryotically with the sequence of their whole open reading frame. Immunoprecipitation and Western blotting showed that the NF-κB pathway was activated in U. unicinctus exposed to sulfide, in which the content of UuNEMO ubiquitination and nuclear Uup65 increased significantly (p < 0.05) in hindgut tissue of U. unicinctus exposed to sulfide. Furthermore, the mRNA level of UuBcl-xL, a downstream anti-apoptosis gene of the NF-κB pathway, increased significantly (p < 0.05) from 48 h to 72 h and the mRNA level of UuBax, a Bcl-xL antagonist gene, decreased significantly (p < 0.05) at 48 h in the hindgut of U. unicinctus exposed to 50 μM sulfide. During the 150 μM sulfide exposure, the level of UuBcl-xL showed no obvious change, whereas the UuBax mRNA level increased significantly (p < 0.05) at 72 h post-exposure to 150 μM sulfide. We suggested that the activated NF-κB pathway up-regulates UuBcl-xL expression, and evokes an anti-apoptotic response to resist sulfide damage at 50 μM in U. unicinctus. Meanwhile, a Bax-mediated pro-apoptotic response occurs when U. unicinctus is exposed to 150 μM sulfide.