He graduated early from the United States Naval Academy in 1941 because the Navy needed officers in the fleet in preparation for World War II. His first assignment was to the U.S.S Lexington which was sunk at the Battle of the Coral Sea. After surviving that battle, he returned to San Francisco where he promptly asked Eleanor Bushnell Yount to be his wife. She flew out from Norristown, PA on a DC3 to marry him on June 26, 1942.

His service in World War II included convoy duty in the Atlantic where his ship, the USS Champlin sank three German submarines and participated in the Sicilian occupation, the bombardments of the Formia-Anzio area of Italy, and the invasion of southern France.

After WWII, he received a Master of Science degree from the Massachusetts Institute of Technology. He then served in the Korean War as the Executive Officer of the USS Shelton and Commanding Officer of the USS Porterfield. After the Korean War, he was the Executive Officer of the USS Salem, Flagship of the Sixth Fleet, operating in the Mediterranean in 1957.

When he attained the rank of Captain, he supervised the construction and assumed command of one of the first guided missile frigates, the USS Leahy. As an Admiral, he assumed command of Cruiser-Destroyer Flotilla Nine and Cruiser-Destroyer Group, Seventh Fleet during the Vietnam War.

His shore duties included Deputy Director for Operations in the National Military Command Center, Project Manager of the Major Surface Combatant Ships Project and Vice Chief of Naval Material.

During his military career, Robert Baughan, Jr. was always active in his family's churches and the Officers' Christian Fellowship. After he retired in 1975, he became treasurer and administrative officer of the Central Pennsylvania Synod of the Lutheran Church. At the age of 60, he entered the Lutheran Theological Seminary at Gettysburg, was ordained in 1981, and called to be the pastor of two churches at the same time, St. John and St. Luke Lutheran Churches in Green Village and Scotland, PA.

In 1994, he fully retired to travel and enjoy life with Eleanor at Cumberland Crossings, Carlisle. In addition to Eleanor, he is survived by two sons, Dr. George R. (wife, Jane) Baughan, Ed.D. of Drexel Hill and Thomas H. (wife, Cynthia) Baughan of North Potomac, MD; one sister, Barbara Sharp of Wooster, OH; grandchildren, Daniel, Michael, Brian, Frank and Edward, Jeremie and Bristol Baughan, Jesseca Brown, Mariah Muhlbradt; and seven great-grandchildren, Casey, Madelyn, Lindsey, Dylan, Callie, Ella and David. He was predeceased by one son, Dr. David M. Baughan, MD, who died Dec. 9, 2012.

Funeral services will be held on Monday, Jan. 13, 2014, at 11 a.m. in the Trindle Spring Lutheran Church, 14 State Rd., Mechanicsburg, with Pastor Richard G. Lorenz officiating. Visitation will be from 10 a.m. until time of services. Burial will be on Tuesday at 12:00 noon in Augustus Lutheran Cemetery in Trappe, PA. Ewing Brothers Funeral Home, Carlisle, is in charge of arrangements.