Neuropeptide FF (NPFF) is one of the members of RF-amide peptide family, which has been implicated in diverse physiological processes across mammals. However, there is scarce information regarding the biological function of NPFF in fish reproduction. In the current study, npff was identified and characterized in the half-smooth tongue sole. The NPFF precursor consisted of one signal peptide and two mature peptides, designated as NPFF and NPAF. Analysis of tissue distribution indicated that npff exhibited high expression levels in the brain and pituitary, while its mRNA levels were much lower in other peripheral tissues. Subsequently, the possible function of NPFF and NPAF on the brain-pituitary-gonad reproductive axis was studied in this species by intraperitoneal injection. At the brain level, both NPFF and NPAF had an inhibitory influence on the levels of transcripts corresponding to kiss1, kiss1r, kiss2, gnrh3, spx1, pnx, gpr173a, and gpr173b. NPFF reduced gnrh2 mRNA levels, but promoted gnihr expression. Moreover, NPAF down-regulated gnih and tac3 expression. At the pituitary levels, gh, gthα, and fshβ mRNA levels were suppressed by NPFF and NPAF, whereas lhβ mRNA levels were elevated. In the ovary, these two peptides stimulated expression of star, p450c17, and fshr. Likewise, NPFF increased 17β-hsd and lhr mRNA levels, and NPAF stimulated p450arom transcript levels. However, 3β-hsd was inhibited by NPFF. Overall, our results suggest that NPFF and NPAF may play distinct roles in control of reproduction of half-smooth tongue sole at multiple levels of the brain-pituitary-ovarian axis.