The prevalence of migraines in females is 3 times greater than in males. Current research has implicated the calcitonin gene-related peptide (CGRP) as a significant factor in the pathophysiology of migraines. This study investigated the sex differences associated with the expression of three protein components of the calcitonin gene-related peptide receptor: calcitonin receptor-like receptor (CLR), receptor activity-modifying protein 1 (RAMP1), and receptor component protein (RCP). The research included comparing baseline protein levels in the spinal trigeminal nucleus caudalis (SpVc) and upper cervical spinal cord between male and female rats and whether or not knock-down of the expression of RCP in the SpVc mitigates pain induced by chemical noxious stimulation of the meninges. The dataset includes western blot images (embedded within the associated article), protein expression analysis, and data associated with pain assessment and tests of facial mechanical hypersensitivity and allodynia in males versus females.