Estrogen (E) and progesterone (P), acting through their respective receptors and other nuclear proteins, exhibit opposing activities in target cells. We previously reported that Krüppel-like factor 9 (KLF9) cooperates with progesterone receptor (PR) to facilitate P-dependent gene transcription in uterine epithelial cells. Here we evaluated whether KLF9 may further support PR function by directly opposing estrogen receptor (ER) signaling. Using human Ishikawa endometrial epithelial cells, we showed that 17-estradiol (E₂)-dependent down-regulation of ER expression was reversed by a small interfering RNA (siRNA) to KLF9. Transcription assays with the E₂-sensitive 4xERE-TK-promoter-luciferase reporter gene demonstrated inhibition of ligand-dependent ER transactivation with ectopic KLF9 expression. E₂ induced PR-A/B and PR-B isoform expression in the absence of effects on KLF9 levels. Addition of KLF9 siRNA augmented E₂-induction of PR-A/B while abrogating that of PR-B, indicating selective E₂-mediated inhibition of PR-A by KLF9.Chromatin immunoprecipitation of the ER minimal promoter demonstrated KLF9 promotion of E₂-dependent ER association to a region containing functional GC-rich motifs. KLF9 inhibited the recruitment of the ER co-activator Sp1 to the PR proximal promoter region containing a half-ERE and GC-rich sites, but had no effect on Sp1 association to the PR distal promoter region containing GC-rich sequences. In vivo association of KLF9 and Sp1, but not of ER with KLF9 or Sp1, was observed in control and E₂-treated cells. Our data identify KLF9 as a transcriptional repressor of ER signaling and suggest that it may function at the node of PR and ER genomic pathways to influence cell proliferation.