The early history of Kalpeni, like much of Lakshadweep, is steeped in legends tying its first settlers to the ancient Chera dynasty of the Malabar Coast. According to local lore, the islands were discovered by shipwrecked sailors during the reign of the legendary king Cheraman Perumal. Historical consensus points to early settlements by Hindus from the Kerala coast, who later converted to Islam around the 7th century following the arrival of the Arab saint Ubaidullah.
During the medieval period, Kalpeni fell under the control of the Arakkal kingdom (the Ali Rajahs of Cannanore), the only Muslim royalty of Kerala. By the late 18th century, sovereignty shifted to the legendary Tipu Sultan of Mysore, and subsequently, to the British East India Company.
A defining moment in Kalpeni's history was the great cyclone of 1847, which drastically reshaped the island's topography by depositing a massive bank of coral boulders along its eastern shore. Following India's independence in 1947, Kalpeni became part of the Republic of India and was formally integrated into the newly established Union Territory of Lakshadweep in 1956. Since then, the island has seen steady socio-economic development while carefully preserving its fragile ecosystem and deeply rooted cultural heritage.