In 1849, when Dalhousie was choosing the ablest Indian officials for the task of organising the Punjaub, Thornton was appointed a commissioner and placed at Rawul Pindi in the Jhelum division.
In 1852 he distinguished himself by his promptitude and courage in arresting Nadir Khan, a discontented son of the raja of Mandla, who was endeavouring to promote a rising of the hill tribes.
Thornton was constantly with him, ably seconding his measures, and he afterwards gave interesting details of Lawrence's conduct at that anxious time, which have been preserved in Bosworth Smith's ‘Life of Lord Lawrence.’ After Lawrence had denuded the Punjaub of troops to assist in the operations against Delhi, Thornton was called on to exercise more independent authority.
In the beginning of September 1857 the intelligence reached Lady Lawrence at Murri that the tribes in the lower Hazarah country contemplated revolt.
She communicated the intelligence to Thornton, who succeeded in arresting the leaders of the conspiracy within a few hours, and by this prompt action prevented any attempt at rebellion.
On the conclusion of the mutiny Thornton was appointed judicial commissioner for the Punjaub, and on 18 May 1860 he was made a companion of the Bath in recognition of his services.
Thornton also contributed to the eighth edition of the ‘Encyclopædia Britannica’ the articles on Bombay, Bengal, Ganges, Nepaul, and, in conjunction with David Buchanan, those on Afghanistan and Burmah.