He was at first affiliated with the American Fur Company, founded by John Jacob Astor, but after 1838 he set up as an independent trader, based in St. Louis, Missouri.
Aitken worked as a clerk in John Jacob Astor's American Fur Company; he was assigned to William Morrison's Fond du Lac Department.
Aitken set up in competition as an independent trader on the Upper Mississippi, based in St. Louis, Missouri.
He was buried on the east bank of the Mississippi opposite to the mouth of the Swan River in Morrison County, Minnesota, where he had a trading post from 1842 until his death.
His daughter Mathilda Aitken married William Whipple Warren, who became a historian of the Ojibwe.