Acute kidney injury (AKI) is associated with poor patient outcome and a global burden for end-stage renal disease. Ischemia-reperfusion injury (IRI) is one of the major causes of AKI, and experimental work has revealed many details of the inflammatory response in the kidney. Here, we investigated whether deletion of the NF-B kinases IKK2 or NEMO in lymphocytes or systemic inhibition of IKK2 would cause different kidney inflammatory responses after IRI induction. Serum creatinine, BUN level and renal tubular injury score were significantly increased in CD4creIKK2f/f (CD4xIKK2) and CD4creNEMOf/f (CD4xNEMO) mice compared with CD4cre mice after IRI induction. The frequency of Th17 cells infiltrating the kidneys of CD4xIKK2 or CD4xNEMO mice was also significantly increased at all time points. CCL20, an important chemokine in Th17 cell recruitment, was significantly increased at early time points after the induction of IRI. IL1β, TNFα and CCL2 were also significantly increased in different patterns. A specific IKK2 inhibitor, KINK-1, reduced BUN and serum creatinine compared with non-treated mice after IRI induction, but the frequency of kidney Th17 cells was also significantly increased. In conclusion, although systemic IKK2 inhibition improved kidney function, lymphocyte-specific deletion of IKK2 or NEMO aggravated kidney injury after IRI, and in both conditions, the percentage of Th17 cells was increased. Our findings demonstrate the critical role of the NF-B pathway in Th17 activation, which advises caution when using systemic IKK2 inhibitors in patients with kidney injury as they might impair the T cell response and aggravate renal disease.