In the spring and summer of 1864, Union officers of the Department of the South on Hilton Head Island became concerned about retaining sufficient troops and equipment to defend Hilton Head, as units were being transferred to participate in campaigns elsewhere, particularly in Virginia and Georgia, where General William Tecumseh Sherman's army had attacked Atlanta in the spring of 1864. Commanders on Hilton Head worried that the Confederates would engage in raids or more serious attacks on the island, especially on the new freedman's village of Mitchelville. Major General John G. Foster ordered Captain Charles R. Suter, Chief of Engineers in the Department of the South, to build an earthwork fort for the purpose of defending Mitchelville and Hilton Head. The pentagonal earthwork was designed to defend the two main approaches to Mitchelville from the southwest and southeast.
Fort Howell did not see action, and was abandoned at wars end. One of the best preserved Civil War earthen forts in South Carolina, it was listed on the National Register of Historic Places in 2011, and was designated as a National Underground Railroad Network to Freedom site by the National Park Service in 2013.