Stephen won the medical journalist of the year category, for journalists writing for a professional audience. He was awarded the prize at an event at the Royal Society of Medicine in London on Tuesday. He had also been shortlisted for another award earlier this year.
The winners of the awards are decided in an 'Oscars'-style voting system, with votes cast by Medical Journalists' Association members.
The medical journalist of the year prize is awarded for a journalist's work over a year, during which Stephen revealed how practices faced losing six figures sums from income because of unforeseen changes to their contracts.
Stephen's article about the failings of care for people with dementia highlighted how half of PCTs could not account for their share of £60 million allocated under the National Dementia Strategy. Last September, he explored how short-sighted budget cuts had denied patients access to life-changing obesity surgery.
Stephen's win follows a run of awards for GP's writers. GP columnist Dr Liam Farrell won best health or medical column for his work on GP at the Medical Journalists' Association Winter Awards early this year. GP's Tom Moberly won the medical journalist of the year award in 2009.
Also, last month, GP's publishing company Haymarket Business Media won the Association of Online Publishers award for Best Digital Publisher of the Year for business publishing.