Early and late metestrus in the rat differ by progesterone levels. As it is known that progesterone shows a potential negative effect on cognitive performances and can counteract the estradiol-induced neural effects, we intended to study signaling proteins in the hippocampus, a structure representing a main brain area of cognitive function. Female OFA Sprague-Dawley rats were used in the studies and estrous phases were determined using vaginal smears. Hippocampal tissue was taken, proteins extracted, run on two-dimensional gel electrophoresis and proteins were identified by mass spectrometry methods (MALDI-TOF-TOF and nano-LC-ESI-MS/MS). Individual signaling protein levels quantified by specific software were shown to vary between the two phases, including NG,NG-dimethylarginine dimethylaminohydrolase 1 for nitric oxide signaling, guanine nucleotide-binding proteins, septin 6, septin 11, G-septin alpha, and 14-3-3 protein gamma. Results from this study indicate that early and late metestrus show differences in signaling pathways, that may help to design further investigations at the protein level and may assist to interpret literature on protein expression and brain protein levels in female rats. Moreover, signaling differences in hippocampus are challenging cognitive studies during these two metestrus phases probably revealing cognitive differences between early and late metestrus.