Robert Emmet McDonald was born in Cabarrus County, North Carolina, in 1842, the son of John McDonald and Caroline Dungan, both of whom had been born in the north.
In 1862 he entered the University of Pennsylvania as a sophomore member of the Class of 1865. His second cousin James Madison Power Wallace was also a member of the Class of 1865. During his college years, McDonald became a moderator of the Philomathean Society as well as his class historian. Despite his southern birth, he served in the Pennsylvania militia during the Civil War emergencies of 1862 and 1863.
McDonald married Ellen Carr of Charlottesville, Virginia. He studied law before settling in Charlotte, North Carolina, where he became a farmer and Justice of the Peace.