Mitogen-activated protein kinase 14 (MAPK14) has a fundamental role in the development of different inflammatory and neurodegenerative disorders. However, its roles in the pathoetiology of migraine are not clear. The current case-control study focused on expression analysis of MAPK14 and related long non-coding RNAs (lncRNAs) in the circulation of migraineurs compared with healthy controls. Data showed remarkable elevation of expression levels of MAPK14, HLA Complex Group 11 (HCG11), zinc ribbon domain-containing 1-antisense 1 (ZNRD1-AS1), RAD51 antisense RNA 1 (RAD51-AS1) and long noncoding RNA-activated by DNA damage (NORAD) in both groups of migraineurs (with aura and without aura) compared with controls. The accuracy of expression levels of MAPK14, HCG11, ZNRD1-AS1, RAD51-AS1 and NORAD for differentiating migraineurs from controls was 85.71%, 81.56%, 85.11%, 77.8% and 94.33%, respectively. Thus, MAPK14 and its related lncRNAs are putative markers for migraine and might participate in the pathogenesis of this neurologic condition.