He and his wife Flavil had one son, Mark Boyd. He has two granchildren, Heather and Alan Boyd. The latter was named after him.
Alan S. Boyd retired to Florida and later moved to Edmonds, Washington.
When the Richard M. Nixon administration took power, Boyd left the government and became the president of the Illinois Central Railroad, a position he held from 1969 to 1972. and the president of Airbus Industries. In 1979 he became the chairman of Warner Blue & Mahan, a Washington D.C. based consulting firm working on new technology ventures.