Enterohemorrhagic Escherichia coli (EHEC) and other attaching/effacing (A/E) bacterial pathogens cause diarrhea in humans. These pathogens use a type III secretion system (T3SS) to inject virulence proteins (effectors) into host cells, some of which inhibit the innate immune system. The EHEC NleH1 effector prevents the nuclear translocation of ribosomal protein S3 (RPS3) to inhibit its participation as a nuclear specifier of nuclear factor kappaB (NF-κB) binding to target gene promoters. NleH1 binds to RPS3 and inhibits its phosphorylation on Ser 209 by the inhibitor of κB (IκB) kinase-β (IKKβ). However, the precise mechanism of this inhibition is unclear. NleH1 possesses a Ser/Thr protein kinase activity that is essential both for its ability to inhibit the RPS3/NF-κB pathway, as well as for full virulence of the A/E mouse pathogen Citrobacter rodentium. However, neither RPS3 nor IKKβ is a substrate of NleH1 kinase activity. We therefore screened ~9,000 human proteins to identify NleH1 kinase substrates and identified the v-crk sarcoma virus CT10 oncogene-like protein (CRKL), a substrate of the BCR/ABL kinase. Knockdown of CRKL abundance prevented NleH1 from inhibiting RPS3 nuclear translocation and NF-κB activity. CRKL residues Tyr 198 and Tyr 207 were required for interaction with NleH1. Lys 159, the kinase active site of NleH1, was necessary for its interaction with CRKL. We also identified CRKL as an IKKβ interaction partner, mediated by CRKL Tyr 198. We propose that the CRKL interaction with IKKβ recruits NleH1 to the IKKβ complex where NleH1 then inhibits the RPS3/NF-κB pathway.