Previous studies have demonstrated ‘quality‐quantity’ trade‐offs with daily food availability times in zebra finches. Compared with food access ad lib., zebra finch pairs with restricted food access for 4 hours in the morning produced poor quality offspring, whereas those with the same food access in the evening produced fewer but better quality offspring. The present study investigated whether food‐time‐dependent differential effects on reproductive performance involved brain peptides associated with reproduction and energy homeostasis in zebra finches. We measured peptide/protein expression of gonadotrophin‐releasing hormone (GnRH)‐I, GnRH‐II, gonadotrophin‐inhibitory hormone (GnIH), tyrosine hydroxylase (TH), neuropeptide Y (NPY), cocaine‐ and amphetamine regulated transcript (CART) and ZENK (a neuronal activation marker) by immunohistochemistry and mRNA expression of genes coding for the type 2 (DIO2) and type 3 (DIO3) deiodinase by a quantitative polymerase chain reaction in male and female zebra finches that were paired and kept under a 12:12 hour light/dark photocycle at 24 ± 2°C temperature for > 12 months with access to food ad lib., or for only 4 hours in the morning or evening. In both sexes, GnRH‐I, DIO2 and DIO3 expression did not differ significantly between the three feeding conditions, although levels showed an overall food effect. However, in males, GnIH expression was significantly higher in evening‐fed birds compared to ad lib. fed birds. Interestingly, GnRH‐II and TH levels were significantly lower in restricted feeding compared to the ad lib. group and, importantly, GnRH‐II and TH‐immunoreactivity levels were negatively and positively correlated with egg laying latency and reproductive success (offspring/brood/pair), respectively. At the same time, we found no effect on the hypothalamic expression of orexigenic (NPY) and anorexigenic (CART) peptides, or ZENK protein (ie, the neuronal activity marker). These results suggest the involvement of reproductive neuropeptides, with putative roles for GnRH‐II and TH, in the food‐time‐dependent effect on reproductive performance, albeit with subtle sex differences, in diurnal zebra finches, which possess the ability to reproduce year‐round, in a manner similar to other continuously breeding vertebrates.