Winthrop was originally a pine tree plantation owned by the University of Western Australia. The first blocks went up for sale in the early 1980s. After the first residents moved in, more blocks were sold off in a number of phases. Shortly after the first residents, a convenience store opened for business. Soon the Winthrop Primary school and Winthrop village shopping centre were opened. Blocks were so sought after that many people resorted to sleeping near the sales office for up to a week just to secure a position.

The name is most likely derived from that of the first Chancellor of the University of Western Australia, Sir John Winthrop Hackett. There are very few reminders of Winthrop's past as a pine plantation, with scattered remnants of pine trees being the only indication.