Estrogens play a pivotal role in breast cancer etiology, and endocrine therapy remains the main first line treatment for estrogen receptor‐alpha (
ER
α)‐positive breast cancer.
ER
are transcription factors whose activity is finely regulated by various regulatory complexes, including histone deacetylases (HDACs). Here, we investigated the role of
HDAC
9 in
ER
α signaling and response to antiestrogens in breast cancer cells. Various Michigan Cancer Foundation‐7 (
MCF
7) breast cancer cell lines that overexpress class
II
a
HDAC
9 or that are resistant to the partial antiestrogen 4‐hydroxy‐tamoxifen (OHTam) were used to study phenotypic changes in response to
ER
ligands by using transcriptomic and gene set enrichment analyses. Kaplan–Meier survival analyses were performed using public transcriptomic datasets from human breast cancer biopsies. In
MCF
7 breast cancer cells,
HDAC
9 decreased
ER
α
mRNA
and protein expression and inhibited its transcriptional activity. Conversely,
HDAC
9
mRNA
was strongly overexpressed in
OHT
am‐resistant
MCF
7 cells and in
ER
α‐negative breast tumor cell lines. Moreover,
HDAC
9‐overexpressing cells were less sensitive to
OHT
am antiproliferative effects compared with parental
MCF
7 cells. Several genes (including
MUC
1,
SMC
3 and S100P) were similarly deregulated in
OHT
am‐resistant and in
HDAC
9‐overexpressing
MCF
7 cells. Finally,
HDAC
9 expression was positively associated with genes upregulated in endocrine therapy‐resistant breast cancers and high
HDAC
9 levels were associated with worse prognosis in patients treated with
OHT
am. These results demonstrate the complex interactions of class
II
a
HDAC
9 with
ER
α signaling in breast cancer cells and its effect on the response to hormone therapy.