John Stewart was the son of Cornelius Stewart, Surgeon of Dunblane.
Arrival in Australia
He arrived in Port Phillip as Surgeon Superintendent on the William Abrams in 1841. Soon afterwards he began advertising a series of Lectures on Phrenology which were to be held in the Royal Exchange Hotel.  He kept his cabin on the ship however and sailed on her to Sydney arriving there in September.
John Stewart's medical practice was established at Captain Pattison's Rose Cottage, west of the Post Office in Morpeth by 1843. He fitted up one of the rooms of his house for the purpose of dispensing and retailing medicine. He claimed that he had never been accused of either forgetting the claims of the poor, or making exorbitant demands on the wealthy.
In January 1844 he married Helena Poynz at Morpeth at the residence of Captain Pattison. Soon afterwards he advertised to receive one or two young gentlemen boarders into his home. A son was born to John and Helena Stewart on 23 December 1844.
In January 1845 he had a lucky escape from injury ......... 'Yesterday evening week an accident occurred to Dr. Stewart, of Morpeth, in crossing Mr. McDougall's punt. this gentleman was about to cross with his friend Mr. Gibbs, in a gig, to Maitland. On the horse touching the punt with its fore feet it receded, when the animal was precipitated into deep water and was drowned. Dr. Stewart saved himself by jumping from the gig as it was sinking. Mr. Gibbs, luckily had adopted the precaution of alighting from the vehicle prior to its descent to the river. 
By June 1845 John and Helen Stewart had moved to Newcastle. Dr. Stewart gave a series of lectures on Phrenology and Human Physiology at the Mechanics Institute at Newcastle in June, July and October 1845. He was presented with a gold watch in thanks for the lectures. The watch was engraved : Presented to Dr. John Stewart, son of Cornelius Stewart Esq., Surgeon Dunblane, Scotland, for his course of lectures on Phrenology at the Mechanics Institute, Newcastle by the members and other friends: Rev. C.P.N. Wilton M.A., President of the Institute. September 1845. 
For a brief few years he was prominent in community and social events at Newcastle.....
In 1845 he campaigned for a Benevolent Asylum and in 1846 he joined those calling for Newcastle to be established as a free warehousing port. In 1847 he assisted in the arrangements for the reception of Sir Charles Fitzroy at Newcastle.
A daughter was born to John and Helena Stewart at Newcastle on 1 April 1846. 
Departure From Australia
In March at Newcastle he came into conflict with Magistrate James Henry Crummer when his post mortem of Findlay Kerr was deemed inadequate.  The following month, April 1847 John Stewart departed Newcastle for Singapore on the Regia. There is no mention of his wife accompanying him.