Junior Doctor Salary. The average salary for a Junior Doctor in the UK is: £33,289. Job profile for a Junior Doctor-we do not currently have a job profile for this role on site, if you are able to write one then please Send it to us-you will be fully credited on site.In 2008, the average salary for this job was £44,424.he average salary in 2011 was £33,144, based on 12 respondents (a difference of 51% from the 2010 figure. The average salary in 2012 was £33,333, based on 3 respondents (a difference of 1% from the 2011 figure. The median salary for a Junior Doctor based on all salary survey responses is: £32,000.