The town was founded in the 5th century BC as Pityus (Ancient Greek: Pityus, Πιτυοῦς, genitive Pityuntos, Πιτυοῦντος) or Pitiunt, a Greek colony and trade port on the coast of the Kingdom of Lazica. Excavations guided by Andria Apakidze unearthed remains of three 4th-century churches and a bath with superb mosaic floors. The former "Great Pityus" harbour is now a mere lake within the town. Saint John Chrysostom was exiled there and died near the shore in 407. Like Dioskurias, it remained under Roman control within the Georgian kingdom of Colchis until the 7th century. The city passed under Abasgian control and became one of the major political and religious centres of the kingdom of Egrisi (Lazica). An archbishopric of Pitiunt was instituted in 541. In medieval Georgia, the town's name was spelled as Bichvinta. At the end of the 10th century, King Bagrat III of Georgia built there the Pitsunda Cathedral which survives to this day and contains vestiges of wall-painting from the 13th and the 16th centuries. Bichvinta also served as the seat of the Georgian OrthodoxCatholicate of Abkhazia until the late 16th century when Abkhazia came under the Ottoman hegemony within Georgia. In his 1911 article for the Catholic Encyclopedia, Sophrone Pétridès described Pityus as a titular see, but it is not now found in the Catholic Church's list of such sees. In the late 13th century, the area housed a short-lived Genoese trade colony called Pezonda.
Pitsunda was the favourite resort of First Secretary of the Communist Party of the Soviet Union Nikita Khrushchev. In October 1964 he happened to be vacationing in Pitsunda when he was deposed from power. Khrushchev once proposed a major dam and hydroelectric power scheme on the Bzyb River near Pitsunda, but his experts informed him that a dam built on the Bzyb River would have had catastrophic effects in causing beach erosion at Pitsunda. In the end, the dam was built on the Inguri River instead, where the impact upon the coastline was assessed to be considerably less pronounced.
On 8 February 2007, after many appeals by inhabitants, the People's Assembly of Abkhazia resolved to give Pitsunda town-status. Parliamentarians expressed the hope that the decision would help Pitsunda develop as a resort. Since becoming a town, the Mayor of Pitsunda is no longer appointed by the Governor of Gagra District but instead directly by the Separatist President of Abkhazia.
In the 2011 so-called assembly elections, separatist Mayor Beslan Ardzinba and six other so-called incumbent deputies of the Assembly stood for re-election. The winning separatist candidates were Beslan Ardzinba, Badra Avidzba, Olga Grigorenko, Chengiz Bigvava, Georgi Zardania, Gennadi Cherkezia, Gennadi Mikanba, Damia Kokoskeria and Inessa Dzkuia. On 14 February, during the first session of the new convocation, Damir Kokoskeria was elected Chairman of the Assembly over Gennadi Cherkezia, by a one vote difference.