Green Island Brook is named in part for a small, grassy offshore island adjacent to the mainland and in part, for the brook which runs through the community into the sea. According to P.A. Thornton, Strait of Belle Isle settlements such as Green Island Brook were founded by Newfoundlanders who claimed their settlement sites (mainly to prosecute the cod fishery) between settlements which had been established by English pioneers in the early Nineteenth Century. In this case Green Island Brook was settled in the 1880s by two families named Macey and Noseworthy between the older settlements of Green Island Cove and Eddies Cove East, although there is evidence that the site was seasonally occupied before this time.

Throughout its history Green island Brook, like other nearby communities, has been dependent on Flower's Cove, which functioned as the region's medical, business, administrative and services centre, for many of its needs.