He was editor of the Harvard Graduates' Magazine from its foundation in 1892 until 1915. In 1903, at the International Historical Congress at Rome, he represented both Harvard University and the American Historical Association, and in 1906 was their representative at the Italian Historical Congress in Milan. In 1902, he was made Knight of the Order of the Crown of Italy, and in 1917 Knight of the Order of Saints Maurizio and Lazaro. In 1914, he was elected to The American Academy of Arts and Letters and he received honorary degrees from Harvard, Yale, Brown and other universities. Thayer served as a member of the Harvard Board of Overseers from 1913 until 1919. He was president of the American Historical Association 1918-1919.