He served as director of the collection of antique sculpture and vases at the Berlin Museum (1889-?) and also as the director of the antiquarium of the Berlin Museum (1896-?). Kekulé was the nephew of the famous organic chemist Friedrich August Kekulé von Stradonitz (1829-1896). Kekulé studied at the universities of Erlangen under Karl Friedrichs, and at Berlin under Eduard Gerhard, Johann Gustav Droysen (1808-1884), and August Böckh (1785-1867). His time in Rome with Enrico Brunn was quite influential for his later writing. In 1870 he succeeded Otto Jahn, who had died prematurely, at the University of Bonn. His 1879 habilitation was written under Adolf_Furtwängler. In 1889 Kaiser Wilhelm II of Germany personally requested Kekulé to be the antiquities director of the collections in Berlin. In the following year he succeeded Carl Robert at the university in Berlin which he held jointly with the directorship. It was then that the emperor allowed the “von Stradonitz” designation. Kekulé greatly increased the size of the imperial collections through a combination of astute buying and commissioning excavations, assisted in the latter by Theodore Wiegand. Kekulé was a prominent lecturer though his writings are tinged with what today appear as superficial comments. His students included Hermann Ulmann and Ulrich von Wilamowitz-Moellendorff (1848-1931).
He eschewed Jahn's "monumental philology" and classification for a methodology closer to Brunn, mixed with an esthetic sensitivity akin to J. J. Winckelmann. His connoisseurship, more than Winckelmann’s, was rooted in scholarship.