Founded in 1819, the building was originally attap mosque built by Bencoolen Muslims. The building was later replaced in 1845 by a permanent version built by an Arab merchant, Syed Omar bin Aljunied. In 2001, due to redevelopment of the area, it was demolished for Somerset Bencoolen, a mixed used residential complex. The mosque itself is integrated into the building and opened in 2004.

The 194-year-old Masjid was originally built between 1825 and 1828 by Indian-Muslim workers who were brought from India to Bengkulu in Indonesia by the British. The mosque is located in a building which also houses offices and shops. Masjid Bencoolen was last renovated in 2004. The plot surrounding the mosque includes a residential apartment tower and commercial wing.