Morgan County was formed in 1822. It was named for Gen. Daniel Morgan, who defeated the British at the Battle of Cowpens in the Revolutionary War. In the late nineteenth and early twentieth centuries, mineral springs in Martinsville gave rise to several spas, and the nickname of the Martinsville High School athletic teams has subsequently been the Artesians. Settlers in Morgan County in the early nineteenth century came predominantly from southern states. The Mooresville area and surrounding communities received large numbers of southern Quakers, driven to migrate because of their opposition to slavery. Paul Hadley, a Mooresville resident, was the designer of the current Indiana flag, as well as a locally prominent water color artist in the early twentieth century. The county courthouse, built in the 1850's, is the oldest in central Indiana.

County government took several steps forward in the 2000's, creating a new Plan Commission, re-instituting a county economic development organization, and establishing the county's first Park and Recreation Board between 2000 and 2004. Morgan County also was the first county in the metropolitan Indianapolis region to establish a smoking ban ordinance for restaurants, taking that step in 2004. Other communities in the region soon followed Morgan County's lead.

A County Achievement Award from the Association of Indiana Counties in 2006 was the third award from the group given to Morgan County in a ten year span, adding to 1997 and 2003 awards.

In 2006 Morgan County was the first in the central Indiana region to offer a prescription drug discount program to its residents at no charge to individuals, helping residents save an average of 20% on prescriptions. Also during 2006, Morgan and Hendricks Counties became the first in Indiana to develop neighboring and co-related TIF (Tax Increment Financing) districts for economic development activity.

Morgan County has developed a new thoroughfare plan that is integrated with the Mooresville thoroughfare plan, and also recently completed a new capital improvement plan. Both activities are preludes to a new comprehensive plan being developed for the county.