Robert Lincoln Kelly served as president from 1903-17. Kelly was educated at Bloomingdale Academy in Parke County, Indiana, graduated from Earlham in 1887, and was a recorded minister. Kelly studied for 3 years at the University of Chicago where he was a student of John Dewey and focused on child psychology. Kelly was a progressive leader for Earlham while working within the Quaker tradition. Entrance requirements were tightened and Kelly sought faculty development by encouraging professors to pursue doctorates.
During Kelly's tenure, a new library was built in 1907 that was praised as the "most perfect" in the state. Fundraising became very important during Kelly's time. Continuing the theme of development, Kelly initiated Earlham into the professional associations that emerged during the Progressive Era. Earlham was a charter member of the North Central Association of Colleges and Secondary Schools in 1915. Kelly also helped found the Association of American Colleges, and was active in the National Education Association. He also helped form a group of Quaker presidents within the Five Years Meeting.
Following his resignation in 1917, Kelly served as executive secretary of the Council of Church Boards of Education, and later as executive secretary of the American Association of Colleges.