We isolated and purified female-specific, sex steroid-responsive peptidergic (FeSP) neurons from intact, sham-operated, and ovariectomized female medaka (Oryzias latipes) and performed RNA sequencing on these neurons (50 neurons per sample, n = 3 for each experimental group). Pairwise differential expression analysis between experimental groups identified genes that are expressed in FeSP neurons in an ovarian-dependent manner.