Hilprecht was born at Hohenerxleben, Germany. He graduated from Herzogl Gymnasium at Bernburg in 1880. He went on to the University of Leipzig where he studied theology, philology, and law, receiving his Ph.D. in 1883. From 1885 to 1886 he became an instructor in Old Testament theology at the University of Erlangen. In 1886 he left for the United States, where he became a professor at the University of Pennsylvania, and the next year in 1887, curator for the Semitic department of its museum. In 1894, Hilprecht took a D. D. degree from the University of Pennsylvania, and an LL. D. from Princeton in 1896. He acted acted as scientific director of four different expeditions to Nippur between 1895 and 1914, and also oversaw the excavation of thousands of historic Sumerian texts from the Temple of the Wind God. From 1893 to 1909 he also reorganised the Babylonian collection of the Imperial Ottoman Museum in Constantinople, while also making several expeditions in Asia Minor and Syria. In 1914 he retired to Germany, before returning to the United States, where he became a citizen.