Between 1919 and 1923, he initially studied law at, successively, universities in Munich, Berlin, and Marburg under faculty who included Heinrich Wölfflin, Adolf Goldschmidt and Werner Weisbach.

He completed his dissertation in Halle under Paul Frankl in 1925 with the title Die Kirchen der Bettelorden in Deutschland (1240–1340).

The same year, while researching at the Bibliotheca Hertziana in Rome, Krautheimer developed the idea for a handbook of Roman churches with a colleague, Rudolf Wittkower, later to become the Corpus Basilicarum.

The ever-declining political situation for Jews in Axis-alliance countries compelled the Krautheimers to emigrate to the United States of America.

At his request, Louisville hired another fleeing art historian, Krautheimer's friend from school days, Justus Bier.

[3] Krautheimer next engaged in what he called his most difficult book to research and write: the survey volume on early Christian architecture for the Pelican History of Art.

The volume turned out to be one of the finest syntheses of late antique/early medieval architecture published and brought Krautheimer his widest readership.

In both cases, Krautheimer selected comparatively neglected periods in Roman history to offer a compelling narrative of the interaction of public works and patronage.

His many students at New York University included Howard Saalman, Leo Steinberg, James S. Ackerman, Frances Huemer, Marvin Trachtenberg, Slobodan Curcic, and Dale Kinney.