Background The comorbidity between rheumatoid arthritis (RA) and migraine is complex and not completely understood. Objective This study aimed to evaluate migraine frequency in patients with RA and its relation to disease activity. Methods A cross-sectional study was carried out on 210 consecutive RA Egyptian patients fulfilling the 2010 EULAR/ACR criteria (joint distribution, serology, symptom duration and acute phase reaction). Results Prevalence of migraine in RA was 28.2%. Disease activity, fibromyalgia and functional losses were significantly higher in migraine group with RA versus non-migraine group (P < 0.001). Disease Activity Score (DAS-28) was independently significant predictor as increasing DAS-28 score was associated with an increased likelihood of exhibiting migraine (5.5-times higher odds per one-unit increase in DAS-28 score). Prevalence of brain MRI white matter hyper-intensities (WMHs) in RA with migraine was 54.8%. WMHs were significantly higher in migraine patients with aura than migraine patients without aura, especially in older patients, longer migraine duration, longer rheumatoid duration and elevated ESR (p < 0.047, p < 0.034, P < 0.004, P < 0.015 and P < 0.22, respectively). Conclusions Migraine is highly frequent in RA patients, especially migraine with aura. The presence of rheumatoid activity, fibromyalgia and secondary Sjogren’s syndrome, elevated ESR and CRP are associated with functional losses in RA patients with migraine, especially migraine with aura. MR imaging of brain is a mandatory tool for detection of white matter hyper-intensities in RA patients with migraine, especially migraine with aura.