Queen Margaret's School for girls beat five other schools to take the award, including other York school, The Mount.
The school was given the award at the independent school of the year awards in London on the 10th of October.
Head teacher Sue Baillie described recieving the award as a 'pleasant surprise' and added that "Everyone gets behind what we do here, it's a great community".
Ms Baillie also credited the success to the newly built Sixth Form study centre which “wouldn’t have been possible without our great and willing estates team".