Having studied theology at the University of Göttingen under Georg Heinrich August Ewald, he established himself there in 1870 as Privatdozent for Old Testament history. In 1872 he was appointed professor ordinarius of theology at Greifswald. Resigning in 1882 for reasons of conscience, he became professor extraordinarius of oriental languages in the faculty of philology at Halle, was elected professor ordinarius at Marburg in 1885, and was transferred to Göttingen in 1892 where he stayed until his death.
Wellhausen was famous for his critical investigations into Old Testament history and the composition of the Hexateuch, the uncompromising scientific attitude he adopted in testing its problems bringing him into antagonism with the older school of biblical interpreters. He is perhaps most well-known for his Prolegomena zur Geschichte Israels of 1883 (first published 1878 as Geschichte Israels), in which he advanced a definitive formulation of the Documentary hypothesis, arguing that the Torah or Pentateuch had its origins in a redaction of four originally independent texts dating from several centuries after the time of Moses, their traditional author. Wellhausen's hypothesis remained the dominant paradigm for Pentateuchal studies until the last quarter of the 20th century, when it began to be challenged by scholars who saw more and more hands at work in the Torah, ascribing them to periods even later than Wellhausen had proposed.
His work on the New Testament, in which he argued for the priority of the Gospel of Mark over the hypothetical source known as Q, was not so well received. (Das Evangelium Marci, übersetzt und erklärt, 1903).
It has been alleged that Wellhausen's scholarship had an antisemitic (and anti-Catholic) component. Wellhausen openly expressed his hostility to the legal (i.e., Jewish) and priestly (i.e., Catholic) portions of the Torah. On learning of Karl Heinrich Graf's hypothesis of the Mosaical law as a late addition to the original spiritual religion of the prophets, Wellhausen was ready to accept Graf's hypothesis "almost before I heard his reasons."
The best known of his works are:
In 1906 appeared Die christliche Religion, mit Einschluss der israelitisch-jüdischen Religion, in collaboration with A Jülicher, Adolf Harnack and others. He also did useful and interesting work as a New Testament commentator. He published Das Evangelium Marci, übersetzt und erklärt in 1903. Das Evangelium Matthäi and Das Evangelium Lucae in 1904 and Einleitung in die drei ersten Evangelien in 1905.