While it is difficult to determine the precise origins of the city, prehistoric remains found in the area have dated human settlement to the middle Paleolithic era (100,000-40,000 B.C.), as well as to the Chalcolithic era (4500–3500 B.C.) and the Bronze Age (3500-1200 B.C.).

The earliest texts mentioning Batroun are the Amarna Letters (mid-2nd millennium B.C.), sent by the governors of the coastal Canaanite cities to the Pharaohs of Egypt to ask for help in repelling Amorite intruders (nomad tribes originating from the middle-Euphratus region in the north). Batroun was subsequently destroyed by the Amorites and remained in ruins until the Tyrian re-colonization in the 9th century B.C. In 7th century B.C., Batroun was among the cities conquered by the Assyrian army.

Batroun was also involved in the war between the successors of Alexander the Great in early 200 B.C. Taking advantage of the disruption and chaos that marked the end of the Seleucids (305 and 64 B.C.), the Itureans (Arab tribes) spread their power over the region from the Békaa and transformed Batroun into a base for their raids against the coastal cities.

By 64-63 B.C., the Roman General Pompey took over the region, and took back Batroun from the Iturean princedom. During the Roman period, Batroun used vinery symbols on its coinage to accredit the etymology of Botrys, its new Greco-Roman name. The currency of Batroun struck during the rule of the Roman emperors Elagabalus (218-222 A.D.) and Alexander Severus (222-235 A.D.) shows that the city had a temple dedicated to a local goddess or Astarte. The construction of a small theatre was launched during the same period but was never completed.

On July 9th, 551 A.D., a violent earthquake struck and destroyed hundreds of Levantine cities, including Batroun. The city did not recover from this catastrophe, and disappeared completely from the historical records until the 12th century A.D.

On the eve of the Crusades, Batroun was part of the Emirate of Banu Ammar, who ruled North Lebanon from the mid-11th century. Batroun was brought down by the Crusaders and became part of the County of Tripoli by 1110. According to some texts, Batroun's fortifications were very weak during this epoch; consequently, the houses were built close together, transforming the city into an easily defendable, compact “building block.” A fort was erected in the center of the city, where some of its remains are still clearly visible today.

Batroun's significance declined during the Mamluke period and remained so until the 19th century. The European travelers of the 17th-18th centuries describe it as "ruined and almost abandoned." By the mid-19th century, Batroun rose from its ashes due to the newly introduced silk industry. The major historic buildings we see today are the best testimony of this development.

The Ras Ech-Chaqa'a Promontory

Ras ech-Chaqa‘a, the promontory to the north of Batroun, dominates the sea with its impressive cape acting as a massive natural barrier between the city of Batroun and Tripoli, hence imposing itself as a daring obstacle to all crossing. Its location and history are tightly connected with Batroun's history: the sea wall, the city harbor, and the Mussaylha Fort.

Before the earthquake of 551 A.D., Batroun was an indispensable stopping point in the journey between Tripoli and the southern coastal cities, served by a costal road that followed along the cape connecting the city of Batroun with Tripoli. This road was destroyed by the earthquake, and Batroun was subsequently bypassed with two new roads. This is perhaps the reason why Batroun disappeared from historical records until the 12th century A.D.

The Ras ech-Chaqa'a promontory was described without exception by all the travelers, historians, and geographers who visited the region. Over the millenniums, many different names have been used. The Greek historian Polybius (205/200–120/118 B.C.) was the first to mention the name Theou prosopon, meaning "the Face of God."

Mussaylha Fort

Following the collapse of the Theouprosopon (the Ras ech-Chaqa'a promontory) in 551 A.D., the coastal road completely disappeared and the northern shoreline was transformed into a high sea cliff. Subsequently, a new road bypassing the promontory from the east was constructed to connect Batroun with Tripoli. This road passes through the Nahr el-Jawz valley from the south, then turns around the Ras ech-Chaqa'a promontory, reaching the other side at a spot near El-Heri called "Bab el-Hawa," meaning the "door of the wind." It was strategically important to build forts to secure this road, as well as to ensure communication and traffic control. The Mussaylha Fort was built for this purpose.

The strategic and military importance of the Mussaylha Fort urged numbers of scholars to study its history and architecture. However, evidence is inconclusive as to whether the rock on which the Fort stands was used since early times as a military station.

The Fort does not include in its current construction any element that could be related to an earlier period, even to the Crusades. The construction techniques, the size of the construction stone blocks and their cutting techniques, the low arched doors and windows, in addition to other elements, suggest the 17th century as the earliest date for the current Fort to have been built. The year 1624 is established by both historians and eye witnesses as the construction date of Mussaylha by Fakhr ed-Dine II. Even if the strategic importance of the site of Mussaylha was exploited since antiquity, the actual state of the Fort cannot be dated earlier than the 17th century.

Koubba

The village of Koubba, on the coast 2 kilometers north of Batroun, is situated in a wooded landscape just north of the river Nahr el-Jawz, with a small Crusader church built on the top of a little hill.