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 stated soon after beginning his practise at Morpeth 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  and soon after was advertising to receive one or two young gentlemen boarders into his family at Morpeth

A son was born to John and Helena on 23 December 1844 and soon after in January 1845, John Stewart had a lucky escape when his horse drowned in the river. The following account appeared in the Maitland Mercury:

'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.

Dr. Stewart was involved in giving a series of lectures on phrenology and Human Physiology at the Mechanics Institute in Maitland. The following advertisement was in the Maitland Mercury in October 1845

'Doctor John Stewart will deliver the first of a series of lectures upon Human Physiology, as the principles of that science may be applied to the preservation of health - to purposes of education - as they are opposed to medical quackery in its every form, and as they evince Omnipotent design - in the theatre of the Mechanics' Institute, on Thursday next at 7pm.'

In Newcastle he campaigned for a Benevolent Asylum to be established and for the port to be made a free warehousing port. In 1847 he also assisted in the arrangements for the reception of Sir Charles Fitzroy at Newcastle

In April he departed Newcastle for Singapore per Regia and in October 1848 when his only daughter Ellen Amelia died after an illness of three days, he was no longer residing in Newcastle