Ten trustees were named in the charter from Virginia. They were charged with the task of laying off lots of half an acre along with streets and public lots. The trustees could sell the lots and use the proceeds "...in such a manner as they may judge most beneficial for the inhabitants of the said town..."

The trustees were empowered to elect successors for vacancies due to death or other disability, and the trustees did not have to reside in Clarksville to serve. Although this special status of non-resident trustees was challenged at various times in Clarksville's early history as a town, the practice continued for several decades. The original Indiana State Constitution in 1816 provided a special exception for the Town of Clarksville to the requirement that officials live within the boundaries of the communities in which they hold office.

The challenges of Clarksville residents to the self-perpetuating, non-resident trustee system were resolved in the late 19th century. The ten-member board stopped meeting in 1889. However, the three-member board that replaced it still may have consisted of non-residents, as one was appointed by the Floyd County commissioners, one appointed by the Clark County commissioners and one was elected by the residents of Clarksville.

At some point between 1889 and 1937, the board changed again to five members, all residents of the town elected by its citizens. However, records of this change were lost in the 1937 flood.

Two other changes occurred to bring Clarksville government to its present structure. In 1981, the State of Indiana recodified its statutes regarding local government, including changing the structure of town boards. Boards of trustees were designated town councils with council members rather than trustees. In 1990, the Clarksville Town Council expanded its membership from five to seven. The current council consists of one member elected from each of the five voting districts and two at-large members.