He was a graduate of Wheaton College in Wheaton, Illinois, Westminster Theological Seminary in Philadelphia, Pennsylvania (where he was deeply influenced by the thought of Professor Cornelius Van Til), and The Free University of Amsterdam, The Netherlands. It was at the Free University that he was taught by Herman Dooyeweerd and D. H. Th. Vollenhoven, whose ideas relating to the construction of a whole new way of doing philosophy Christianly from a Biblical basis radically changed the direction of his life, and whose teachings he later brought to North America. Runner's dissertation applied D. H. Th. Vollenhoven's problem-historical method to Aristotle's Physics. Runner had also studied at Harvard University, where he was a Junior Fellow of the Society of Fellows, and at the University of Pennsylvania, where he engaged in intensive studies in Greek and Philosophy.
Early in his career at Calvin College he organised the Groen van Prinsterer Society (known popularly as the 'Groen Club'), which brought him together with students specifically interested in discussing issues relating Christianity to culture, and the necessity Runner saw of Christian cultural organization. He was also greatly influential in the setting up of the Association for Reformed Scientific Studies (ARSS) in 1956 - which later became the Association for the Advancement of Christian Scholarship (AACS). The AACS eventually became the Institute for Christian Studies (ICS). The ICS's first senior members were all students of Runner.