After earning his MBA, Harper spent five years at General Motors Corp. in Lansing, Michigan, working in methods engineering. In 1955, he joined the Pillsbury Company in Minneapolis, Minnesota, where he worked for 20 years and rose to the level of group vice-president. In 1974, he joined ConAgra in Nebraska as executive vice-president and chief operating officer. In 1981, Harper became ConAgra's chairman and CEO.

In 1991, business leaders ranked Harper among the top American business masterminds for the remarkable turnaround of ConAgra. Under his leadership, ConAgra diversified and grew, becoming one of the top 20 industrial corporations in the United States. Harper engineered the company's strong rebound from losses in 1974 to $232 million in net income for 1990.

Harper served as a director of Burlington Northern Inc., Norwest Corporation, Peter Kiewit & Sons, and Valmont Industries, Inc. He was a member of the Business Roundtable, a director of the Grocery Manufacturers of America, Inc., a member of the board of trustees of the Committee for Economic Development in Washington DC, a director of the U.S. Chamber of Commerce, and chairman of its Food and Agriculture Committee.