During 1834-1835 he travelled through the sparsely settled country between the Hunter and Namoi Rivers, including the Liverpool Plains, collecting specimens of birds and mammals.

After gaining experience in pastoral management at his brother's property “Yarrundi” near Scone, Coxen was involved in the management of several properties, first in northern New South Wales and later as one of the early settlers of the Darling Downs region of southern Queensland, along with his nephew Henry Coxen.

In 1862 he helped establish the Queensland Museum in Brisbane, became its first honorary curator and secretary, as well as being a trustee, in association with the explorer Sir Augustus Gregory.

Coxen died at Bulimba in Brisbane and was buried in Tingalpa Christ Church (Anglican) cemetery.

There is also Charles Coxen Close, Oxley Vale, a suburb of Tamworth in northern New South Wales.