Gregorovius was the son of Neidenburg district justice council Ferdinand Timotheus Gregorovius and his wife Wilhelmine Charlotte Dorothea Kausch. Gregorovius family members lived for over 300 years in Prussia and had many jurist, preachers and artists. One famous ancestor of Ferdinand's was Johann Adam Gregorovius, born 1681 in Johannisburg, district of Gumbinnen. An earlier ancestor named Grzegorzewski had come to Prussia from Poland.
Ferdinand Gregorovius was born at Neidenburg, East Prussia (now Nidzica, Poland), and studied theology and philosophy at the University of Königsberg. In 1838 he joined the Corps Masovia. After teaching for many years, Gregorovius took up residence in Italy in 1852, remaining in that country for over twenty years. In 1876 he was made honorary citizen of Rome, the first German to be awarded this honor. A street and a square are named after him. He eventually returned to Germany, where he died in Munich.
He is best known for Wanderjahre in Italien, his account of the travels on foot that he took through Italy in the 1850s, and the monumental Die Geschichte der Stadt Rom im Mittelalter (History of Rome in the Middle Ages), a classic for Medieval and early Renaissance history. He also wrote biographies of Pope Alexander VI and Lucrezia Borgia, as well as works on Byzantine history and medieval Athens, and translated Italian authors into German, among them Giovanni Melis. According to Jesuit Father John Hardon, S.J. Gregorovius was "a bitter enemy of the popes."
- Der Ghetto und die Juden in Rom, Mit Einem Geleitwort von Leo Baeck, Im Schocken Verlag/Berlin, 1935 (originally published, 1853)
- Der Tod des Tiberius ("Tiberius' Death", 1851)
- Geschichte des römischen Kaisers Hadrian und seiner Zeit ("History of the Roman Emperor Hadrian and His Times", 1851)
- Siciliana (1853)
- Corsica (1854)
- Göthe’s Wilhelm Meister in seinen socialistischen Elementen entwickelt. Schwäbisch Hall: E. Fischhaber, 1855.
- Geschichte der Stadt Rom im Mittelalter (1859–1872) Translated into English 'The History of Rome in the Middle Ages' (1894–1902). (reissued by Italica Press, 2000–2004.); (reissued by Cambridge University Press, 2010. ISBN 978-1-108-01513-4)
- Wanderjahre in Italien (1856–1877)
- Geschichte der Stadt Athen im Mittelalter. Von der Zeit Justinians bis zur türkischen Eroberung ("History of Athens in the Middle Ages. From Justinian to the Turkish Conquest", 1889)
- Lucretia Borgia und ihre Zeit (Lucrezia Borgia: a chapter from the morals of the Italian Renaissance, 1874)
- Die Grabmäler der Römischen Päpste (The Tombs of The Roman Popes), first edition 1857 in German (Google books link), later in 1881 as Die Grabdenkmäler der Päpste (The Tombs of The Popes) (Open Library link) and in English as The Tombs of the Popes (tr: Louisa W. Terry) Victoria Press, Rome 1904 (Google books link)