After serving for some time as preacher and teacher in Arnswalde, Berliner was called (1865) to Berlin as superintendent of the religious school maintained by the society for Talmudic studies (Ḥebrat Shas), and in 1873, when Israel Hildesheimer opened the rabbinical seminary in Berlin, Berliner was elected professor of Jewish history and literature. In this position, as well as in that of author, he has displayed an untiring activity. His edition of Rashi's commentary to the Pentateuch (1866) first made him known as a scholar; he added to his reputation by various historical works, the result of his studies in the archives and libraries of Italy, which country he frequently visited, subventioned by the German government.

Berliner edited for two years (1874–75) the scientific periodical Magazin für Jüdische Geschichte und Literatur, which from 1876 to 1893 he, together with his colleague, David Hoffmann, continued under the title Magazin für die Wissenschaft des Judenthums. It was due to his zeal that the society Meḳiẓe Nirdamim, for the publication of works of the older Jewish literature, which had been discontinued for several years, was revived in 1885 with Berliner as its director. He further acted as the apologist of Judaism in a pamphlet against Lagarde (Prof. Paul de Lagarde, nach Seiner Natur Gezeichnet, 1887), who denounced all Jewish scholars as dilettanti; and when the blood accusation was revived, he republished (1888) the opinion of Cardinal Ganganelli—afterward Pope Clement XIV—to prove the falsity of this charge.

While orthodox in his religious views, Berliner was never a fanatic. He not only associated in his scientific work with the liberals, but also paid a high tribute to the merits of M. Steinschneider on the occasion of the latter's seventieth birthday (1886), by compiling a bibliography of that eminent scholar's works.