The aim of the study is to describe the severity, temporal characteristics, and types of autonomic features as they relate to the characteristics of pain of the neuralgias. Also, to describe, based on literature, how these autonomic features can affect the treatment outcomes of patients with craniofacial neuralgias. We carried out a literature search using five databases, PubMed, Embase, OVID, Scopus and Web of Science. The search was executed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The protocol for this systematic review and meta-analysis was registered on PROSPERO CRD42021235319. 40% of all patients with craniofacial neuralgias had at least one autonomic feature. Out of the craniofacial neuralgias, trigeminal neuralgia was the most reported, with lacrimation being the most prevalent concomitant autonomic feature. There was also differences in the occurrence of the autonomic features dependent on which branch of a nerve such as the trigeminal nerve, was afflicted. When trigeminal neuralgia is excluded, the rest of the craniofacial neuralgias had reported autonomic features 28% of the pain events. (95% Confidence Interval: 2–90%). Contrary to the conventional belief, we found certain autonomic features to be more predominant than others, in specific craniofacial neuralgias. The prevalence of the autonomic features for all craniofacial neuralgias in the descending order is as follows, lacrimation, conjunctival injection, nasal congestion, rhinorrhea, flushing, edema/swelling, salivation, ptosis and sweating. With trigeminal neuralgia, the most common autonomic feature was lacrimation, and the least common was nasal congestion.