Vernazza's name is derived from the Latin adjective verna meaning "native" and the aptly named indigenous wine, vernaccia ("local" or "ours"), helped give birth to the village's moniker.
First records recognizing Vernazza as a fortified town date back to the year 1080. Referred to as an active maritime base of the Obertenghi, a family of Italian nobility, it was a likely point of departure for naval forces in defence of pirates.
Over the next two centuries Vernazza was vital in Genova's conquest of Liguria, providing port, fleet and soldiers. In 1209, the approximately 90 most powerful families of Vernazza pledged their allegiance to the republic of Genova.
The first documented presence of a church dates back to 1251, with the parish of San Pietro cited in 1267. Reference to the Church of Santa Margherita d'Antiochia of Vernazza occurs in 1318. Some scholars are of the opinion, due to the use of materials and mode of construction, that the actual creation of the Church of Santa Margherita d'Antiochia took place earlier, some time in the 12th century. The Church of Santa Margherita d'Antiochia was expanded upon and renovated over the course of the 16th and 17th centuries, and thereafter was erected the octagonal bell tower that rises from the apse.
In the 1400s Vernazza focused in its defense against the dreadful and regularly occurring pirate raids, erecting a fortifying wall. In the mid-1600s, like many of the Cinque Terre villages, Vernazza suffered a period of decline that negatively affected wine production, and prolonged the construction of the trail system and harbor molo (pier constructed to protect against heavy seas).
In the 1800s, after a long period of stagnation, Vernazza returned to wine production, enlarging and creating new terraced hillsides. The result was a revitalization of Vernazza's commerce. Also at this time the construction of the Genova–La Spezia rail line began, putting an end to Vernazza's long isolation. The population of Vernazza increased by 60% as a result. Meanwhile, the construction of La Spezia's naval base also proved important to Vernazza in providing employment for many members of the community.