It was built in the year 1568 by the MalabarYehudan people or Cochin Jewish community in the Kingdom of Cochin.
The original synagogue was built in the 4th century in Kodungallur (Cranganore) when the Jews had a mercantile role in the South Indian region along the Malabar coast now called Kerala.
A tablet from the earlier synagogue in Kochangadi in Kochi (built in 1344) is placed on the outerwall of the Mattancherry synagogue.
Some sources say that the earliest Jews were those who settled in the Malabar coast during the times of Solomon, and after the Kingdom of Israel split into two.