Thomson succeeds Marcus Brauchli, who resigned from his position as managing editor.
Thomson was previously publisher of Dow Jones, a position he had held since December, following News Corp.â€™s acquisition of Dow Jones. Prior to that, he was editor of The Times of London.
His appointment was unanimously endorsed by the Dow Jones Special Committee following a nomination by the company last week.
Thomson will oversee the news section of The Wall Street Journal and the editorial operations of Dow Jones News Wires.